Trying to run an agency without a reliable time tracking system is like flying a plane with a cracked dashboard. You know you’re moving, but you have no clue how fast, how far, or whether you’re even on course.
You probably know the feeling. You’re spending hours every week chasing timesheets, juggling payroll, and wondering which projects are actually profitable.
At the same time, how do you know if your remote or hybrid team is making the most of their time?
Are you over-servicing some clients without realizing it? Could your agency be leaking billable hours just because the wrong system is in place?
As Brad Yale, SVP at Medical Knowledge Group, explains:
“Timesheets have long been a staple of ad agencies’ billing and project management processes. However, over the years, it has become increasingly clear that timesheets may not be as effective as the agency world perceives them to be.”
So what’s the better way to track employee hours, manage projects, and deliver accurate invoices while helping your team stay focused?
In this article, you’ll discover the best time tracking software for agencies. These tools go beyond basic tracking. They offer features such as workforce analytics, employee time tracking, and productivity insights, whether your team works remotely, in the office, or across a distributed workforce.
But before we dive into the top tools, it’s helpful to first understand what time tracking software for agencies really means. That way, you’ll see why it’s such an essential tool for growing teams.
Table of Contents
- What is employee time tracking software for agencies?
- 8 things you need from time tracking software for agencies
- How to choose the right time tracking software for your agency
- 7 common mistakes agencies make when tracking time
- The top 7 time tracking software for agencies
- Employee time tracking software comparison table
What is employee time tracking software for agencies?
Employee time tracking software for agencies helps you understand exactly how your team spends time on client work, internal tasks, and project deadlines.
Instead of relying on messy spreadsheets or outdated timesheets, this type of software gives you a clear view of daily work patterns. You’ll know:
- When each team member starts and ends their workday
- How long do they spend on specific tasks or projects?
- Which websites and apps do they use during work hours?
- How much time is productive compared to idle time?
- What counts as billable time versus non-billable time?
If you’re managing a remote, hybrid, or in-office agency, this kind of visibility can lead to better team management and more reliable outcomes. You get the insights you need to lead effectively while giving your team the space to work independently.
More importantly, employee time tracking software supports:
- Payroll accuracy for full-time staff and freelancers
- Attendance monitoring that helps you stay on top of schedules
- Screen monitoring features that create accountability and transparency
- Workforce analytics to uncover time-wasting habits and improve workflows
- Better time management for both leadership and employees
When you’re managing a busy agency, it’s not enough to just track time. You need the right software to support your team, improve workflows, and keep clients happy.
So, what exactly should you look for when choosing a time tracking tool?
Let’s break down the 8 must-have features every agency needs.
8 things you need from time tracking software for agencies
When you’re choosing time tracking software for your agency, you need more than a digital stopwatch. The right tool should help you manage people, projects, payroll, and performance, without adding extra work to your day.
Here’s what to look for:
1. Smart automation
The software should start tracking time automatically, without requiring your team to remember to click a button. It should also detect idle time and capture proof of work through screen monitoring features, such as screenshots or screen recordings. This helps improve accuracy and accountability.
2. Flexible tracking modes
Not every agency team works the same way. Some prefer manual tracking, while others need a silent mode that starts when the device powers on. Look for a tool that supports both options, allowing everyone to stay productive.
3. Project and cost tracking
You want a clear view of how long each project takes and how much it’s costing your agency. A good tool helps you estimate timelines, manage budgets, and track time by client or task. That way, you can stop guessing and start making data-backed decisions.
4. Team scheduling and attendance
Managing a remote or hybrid team? You’ll need features like shift scheduling, attendance tracking, and alerts when someone misses a scheduled start. These tools help ensure that projects are appropriately staffed without overexerting anyone.
5. Easy-to-use integrations
Time tracking shouldn’t live in a silo. The best tools seamlessly integrate with your tech stack, including project management platforms, payroll apps, communication tools, and accounting software. Seamless integrations save time and improve your agency’s workflow.
6. Employee-first features
Tracking time is most effective when your team is entirely on board. Look for features that give employees visibility and control, such as blurred screenshots, editable time logs, and opt-in tracking. These options help create a culture of transparency and trust.
7. Productivity analytics
If you want to grow your agency, you need insights, not just data. Choose a platform that offers detailed productivity reports, showing active time, idle time, and time spent on each task. These analytics help you spot bottlenecks and improve team performance.
8. Scalability for growing teams
You might start with a few freelancers or a small team. But as your agency grows, your software should keep up. Look for unlimited projects, long-term data storage, and performance tracking across a distributed workforce.
Finding time tracking software with the right features is a great start. Yet with so many options out there, how do you know which tool is the best fit for your agency’s unique needs?
Let’s walk through a simple way to choose the right time tracking solution with confidence.
How to choose the right time tracking software for your agency
Choosing the best time tracking software for agencies is not just about finding the platform with the most features; it’s also about selecting one that suits your specific needs. It’s about selecting the tool that aligns with how your team actually works every day.
Here’s how to narrow it down based on your team setup:
If your agency is fully remote
You need software that makes employee time tracking feel effortless across time zones. Prioritize tools that offer:
- Automated time tracking without manual input
- Screen monitoring features, such as screenshots or activity tracking, to create transparency
- Productivity analytics that show active time, idle time, and app usage
- Payroll integrations to simplify payments for distributed teams
Look for a tool that gives remote employees control over their privacy settings, such as the ability to blur screenshots or edit time entries. This builds trust while keeping work visible.
If your agency is hybrid
Hybrid teams need flexibility. Some employees work in the office, others work from home. Your software should support both by offering:
- Easy shift scheduling and attendance tracking for on-site staff
- Idle time alerts and auto-start tracking for remote workers
- Integration with project management apps to keep everyone aligned
- Real-time reporting so managers can monitor project progress without micromanaging
Choosing a platform that balances in-office and remote needs will help your hybrid team stay connected and productive, no matter where they work.
If your agency is fully in-office
For agencies where everyone works on-site, you still need a tool that automates manual admin tasks and improves productivity. Focus on finding software that:
- Starts tracking time automatically when work devices power up
- Tracks time across multiple projects and clients with minimal setup
- Provides detailed reports on project costs, billable hours, and employee performance
- Supports team management features like shift planning and attendance monitoring
Finding the right tool is a big step toward improving how your agency manages time and projects. Yet even with great software, it is easy to fall into habits that waste time, hurt productivity, or frustrate your team.
Before you roll out a new time tracking system, it helps to know the common mistakes agencies make, and how you can avoid them.
7 common mistakes agencies make when tracking time
Employee time tracking can help your agency stay profitable and productive, but only if you utilize it effectively. Here are some of the most common mistakes that hold teams back, and what to do about them:
1. Relying on manual timesheets
Manually filling out timesheets leads to guesswork and missing hours. It’s easy to forget what you did at 10 a.m. yesterday, especially in a fast-paced agency.
To fix this, use employee time tracking software that records time automatically in real time.
2. Tracking time without context
Some tools just track hours worked. But without knowing what the time was spent on, the data isn’t that useful.
You’ll get better results with a tool that tracks time by task, client, or project, which improves productivity analytics and billing accuracy.
3. Not reviewing the data
Collecting time tracking data is only part of the equation. Many agencies overlook this analysis and miss opportunities to enhance team performance or minimize wasted time.
Taking time to review reports on attendance, idle time, and project costs can help you identify what’s working and what’s not.
4. Making it feel like surveillance
If time tracking feels like spying, your team won’t buy into it. This can lead to resentment, stress, and even high turnover.
You can avoid this by utilizing user-friendly features, such as blurred screenshots and editable time logs, and being transparent about how time tracking benefits the team, not just management.
5. Ignoring integrations
If your time tracking tool doesn’t connect with your project management or payroll system, you’ll end up with extra admin work.
Choosing a platform with solid integrations makes it easier to manage workflows, invoice faster, and reduce errors.
6. Tracking time but not using it for payroll
Some agencies track time, but still handle payroll manually. This creates more work and increases the chance of errors.
It’s much easier when your time tracking software integrates directly with payroll tools and automates the process.
7. Using the same setup for every team
What works for your in-office staff might frustrate your remote team. Every work environment is different.
That’s why it’s helpful to use a tool that supports all types of work, such as remote, hybrid, and in-office, so every team member has what they need.
Now that you know what to avoid and what features truly matter, the next step is to find the right tool for your team. Whether you manage a remote, hybrid, or in-office agency, the right software can make time tracking simpler and more effective.
The top 7 time tracking software for agencies
Here are seven of the best time tracking software options for agencies to consider.
1. Time Doctor
Time Doctor is an employee time tracking software that works well for agencies managing multiple clients, remote or hybrid teams, and fast-moving projects. It helps you understand how your team works, where time is spent, and how to stay profitable without adding more manual work to your day.
This tool is a strong fit for agencies that need accurate data for payroll, proof of work for clients, and visibility into employee productivity.
Time Doctor features
A. Flexible time tracking modes
Whether your team prefers manual or automatic tracking, Time Doctor supports both. This allows employees to choose how they log their time while still providing you with consistent data.
B. Screen monitoring for accountability
With screenshot capture, screen recording, and idle time tracking, you can confidently show clients how time is spent. At the same time, teams can blur screenshots to protect sensitive client information while keeping transparency.
C. Project- and client-based tracking
You can track time by project, task, or client account. This makes it easier to calculate billable hours and create detailed invoices that clients trust.
D. Productivity analytics
The platform includes reports on active versus idle time, app usage, and task breakdowns. This helps you spot inefficiencies and improve team performance.
E. Attendance and scheduling tools
You can set up recurring or one-off shifts for team members. Attendance tracking confirms when work begins and ends, which is especially helpful for remote or hybrid work environments.
F. Payroll integration
Time Doctor integrates with payroll tools such as Gusto, PayPal, and QuickBooks. It automatically generates timesheets and processes payments, helping reduce admin time during payroll.
You can use the platform to configure pay periods for salaried or hourly employees. You can also use the tool to create timesheets and automate payment processing.
G. Productivity reports
How does your team’s active working time compare to their idle time? How much time are they spending on specific projects or client accounts?
Time Doctor’s time tracking reports provide actionable insights that you can use to find efficiency issues and improve productivity.
With these reports, you can also control project costs and create more accurate forecasts. You can even use them to identify and replace less profitable clients.
H. Employee benchmarking
When you want to level up your team, you need to know what kind of productivity metrics are possible, and how to coach your team to reach them.
Time Doctor’s benchmarking tools highlight your team’s top performers and analyze their workflows. Using these insights, you can reward high-performing employees and help the rest of your team get unstuck and work more efficiently.
I. Experience analysis
If you’re actively growing your agency, then improving productivity is likely a critical goal. Yet working too hard can lead to burnout over time.
With Time Doctor’s work-life balance widget, you can identify the employees putting in too many work hours or showing unusual activity levels.
From there, you can help these team members course-correct. This way, they can improve their
J. Burnout prevention tools
If someone is working unusually long hours or showing unusual activity, the platform flags it. This gives you the opportunity to step in early and support improved time management across your agency.
Pricing
- Basic: $6.70 per user per month (billed annually)
- Standard: $11.70 per user per month with added integrations, payroll, and productivity ratings
- Premium: $16.70 per user per month with screen recordings and client access features
Customer ratings
- Capterra: 4.5 out of 5 (540+ reviews)
- G2: 4.4 out of 5 (400+ reviews)
If your agency is seeking employee time tracking software that fosters accountability, streamlines payroll, and enhances overall productivity, Time Doctor is a reliable choice.
2. RescueTime
RescueTime is a productivity assistant that helps individuals and teams understand how they spend their time. It combines time tracking with goal setting, coaching tools, and distraction blocking.
While it works well for solo professionals or teams looking to improve focus, it may not offer the depth some agencies need for managing billable hours or tracking multiple client projects.
RescueTime features
A. Custom daily focus goals
RescueTime learns from each user’s schedule and activity patterns. It uses this data to suggest focus targets for each day.
B. Productivity coaching
The platform offers insights and tips to help employees stay focused, avoid burnout, and achieve long-term improvements in focus.
C. Focus sessions
Users can block distracting websites and apps for set periods, which helps them stay in a state of deep work.
D. Reporting on habits
The tool tracks focus time, distractions, overwork, and “flow” time. These reports help spot trends in how your team works.
Pricing
- Free version available with limited features
- Paid plans start at $6.50 per user per month
Customer ratings
- Capterra: 4.6 out of 5 (130+ reviews)
- G2: 4.1 out of 5 (80+ reviews)
However, RescueTime doesn’t offer built-in employee time tracking by project or client, which makes it harder to manage billable hours or generate client-ready reports. It also lacks detailed attendance tracking, payroll integrations, and team scheduling features, all of which are essential for growing or distributed agencies.
It focuses more on personal productivity than operational performance, which may limit its usefulness for agency-wide insights or managing team accountability.
3. Harvest
Harvest is a clean, user-friendly time tracking software that helps agencies track billable hours and convert time into invoices. It’s beneficial for teams that need simple tracking with quick access to reports and basic client billing.
Harvest features
A. Easy-to-use time tracker
Offers a straightforward timer that works seamlessly across desktop and mobile, making it easy for team members to log hours wherever they work.
B. Actionable reports
Provides clear reports on how time is spent across projects and tasks. These insights can help agencies better understand workloads and improve planning.
C. Invoicing made easy
Harvest converts tracked hours into client-ready invoices with just a few clicks. This makes it a valuable tool for agencies seeking to streamline their billing processes.
D. Wide range of integrations
Connects with over 50 platforms, including Trello, Asana, and QuickBooks. These integrations enable smoother workflows and reduce the need for manual steps.
Pricing
- Free version available for solo users
- Paid plans start at $10.80 per seat per month (billed annually)
Customer ratings
- Capterra: 4.6 out of 5 (540+ reviews)
- G2: 4.3 out of 5 (775+ reviews)
While Harvest excels in invoicing, it lacks several key features essential for in-depth agency operations. It doesn’t offer screen monitoring, attendance tracking, or employee benchmarking. Without tools like payroll integration or idle time tracking, it can be harder to manage remote or hybrid teams efficiently.
Additionally, if your agency requires more advanced workforce analytics or detailed visibility into daily activity levels, a more comprehensive solution may be necessary.
4. Toggl Track
Toggl Track is a fast and flexible time tracking software that helps teams improve workflows, track billable hours, and get paid faster. It’s ideal for agencies seeking a straightforward and visually clean interface to track time across multiple projects.
Toggl Features
A. One-click time tracking
Toggl Track makes it easy to start and stop timers without interrupting your team’s flow. This is particularly helpful for agencies that juggle multiple tasks throughout the day.
B. Project cost estimates
You can forecast the duration of a project and estimate costs accurately upfront. This feature enables more informed budgeting and pricing decisions for client work.
C. Billable hour tracking
Toggl makes it easy to monitor how much of your team’s time is billable versus non-billable. This helps with profitability and smarter client invoicing.
D. Detailed reports
The platform generates project and team reports that give you insight into workloads and task breakdowns. These can be shared with clients for added transparency.
Pricing
- Free plan available for teams of up to five users
- Paid plans start at $9 per user per month (billed annually)
Customer ratings
- Capterra: 4.7 out of 5 (2,100+ reviews)
- G2: 4.6 out of 5 (1,500+ reviews)
Toggl Track is excellent for simple time tracking, but it doesn’t offer screen monitoring, attendance tracking, or employee benchmarking. There is no built-in payroll integration, either, which may require agencies to use additional tools or manual processes.
For agencies that manage hybrid or remote teams and require stronger productivity analytics, employee time tracking, or tools to monitor idle time, a more comprehensive platform may offer better long-term value.
5. Clockify
Clockify is a well-known time tracker and timesheet tool that helps teams log hours, plan work, and monitor productivity. It’s especially popular with businesses seeking a cost-effective solution for managing time tracking across an unlimited number of users.
For agencies managing multiple clients or large teams, Clockify offers a range of useful features, especially for timekeeping and basic reporting.
Clockify features
A. Automated timers and timesheets
Employees can log their hours using start/stop timers or manually complete timesheets. The calendar view makes it easy to review tracked time by day or week.
B. Team scheduling and task assignments
You can schedule shifts, assign tasks, and track progress across your team. This helps keep client projects organized and on track.
C. Project cost forecasting
Clockify estimates labor costs based on employee rates and hours worked. This makes budgeting easier and helps you price your services more accurately.
D. Reporting and analytics
The platform provides insight into employee activity, time spent on tasks, and team locations. These reports support basic workforce analytics and project reviews.
Pricing
- Free forever plan available with unlimited users
- Paid plans start at $3.99 per user per month (billed annually)
Customer ratings
- Capterra: 4.7 out of 5 (4,400+ reviews)
- G2: 4.5 out of 5 (140+ reviews)
Clockify handles time tracking well, but it doesn’t offer screen monitoring, idle time tracking, or advanced employee benchmarking. If you’re managing a hybrid or remote team and need real-time visibility into how work gets done, those features can make a big difference.
Additionally, while it supports invoicing and expense tracking, it lacks native payroll integration. This means you may need an additional tool to process payments, which adds complexity for agencies that handle multiple freelancers or contractors.
6. Timenotes
Timenotes is a straightforward time tracking and project management tool built for simplicity. It helps solo professionals and small teams log work hours, manage tasks, and generate reports for invoicing.
For small agencies seeking a lightweight solution to track time and manage projects, Timenotes can be a good starting point.
Timenotes features
A. Editable time logs
Team members can track time in real-time or manually adjust time entries, which gives flexibility when working on various projects or clients.
B. Team timesheets
The platform creates monthly team timesheets, helping you monitor attendance and spot trends in how time is spent across your agency.
C. Client invoicing support
Reports can be turned into branded invoices, making it easier to bill clients based on tracked time.
D. Project management integrations
Timenotes integrates with popular tools to streamline your workflow and minimize manual data entry.
Pricing
- Starts at $39 per year for solo users
- Team plans begin at $6.99 per user per month
Customer ratings
- Capterra: 4.4 out of 5 (30+ reviews)
- G2: Not listed
Timenotes lacks screen monitoring, attendance tracking, and payroll integration, which may limit its usefulness for remote or hybrid teams. It also doesn’t offer employee benchmarking or in-depth productivity analytics, so agencies with more complex needs may outgrow it quickly.
7. DeskTime
DeskTime is a time-tracking platform that combines productivity tools with workforce management features. It’s designed to help employers understand how time is spent during the workday and make better decisions about project costs, scheduling, and team efficiency.
For agencies seeking a fully automated time tracker with built-in focus tools, DeskTime offers a practical solution.
DeskTime Features
A. Automatic time tracking
DeskTime starts and stops tracking as soon as the device is in use. This reduces the chance of missed entries and improves accuracy.
B. Screen and app monitoring
The platform tracks URLs, apps, and document titles to give managers a detailed view of work habits. This data supports better employee time tracking and productivity analytics.
C. Project cost estimation
You can assign hourly rates to employees and projects, making it easier to calculate expenses and evaluate client profitability.
D. Pomodoro timer and private time
Built-in break timers encourage healthy work habits, while the private time feature allows employees to pause tracking when needed.
Pricing
DeskTime Lite is free for one user. The platform’s paid plans start at $7/user per month (when billed annually).
Customer ratings
- Capterra: 4.5/5 (475+ reviews
- G2: 4.6/5 (175+ reviews)
Although DeskTime is strong in monitoring and automation, it lacks deeper attendance tracking, payroll integration, and team scheduling features. These tools are essential for agencies managing remote or hybrid teams.
There is also limited flexibility when it comes to customizing time logs or generating detailed, client-ready reports.
For agencies that require scalable time tracking software with enhanced support for project billing, employee benchmarking, and comprehensive workforce analytics, other platforms may offer more extensive functionality.
Employee time tracking software comparison table
| Tool | Key Features | Pricing | Customer Ratings | Best For |
| Time Doctor | Flexible tracking, screen monitoring, project tracking, payroll integration, productivity analytics, employee benchmarking, burnout prevention | Basic: $6.70/mo, Standard: $11.70/mo, Premium: $16.70/mo | Capterra: 4.5/5, G2: 4.4/5 | Agencies needing full visibility, payroll, productivity analytics |
| RescueTime | Focus goals, productivity coaching, distraction blocking, reporting on habits | Free limited version, Paid: $6.50/mo | Capterra: 4.6/5, G2: 4.1/5 | Solo professionals or teams focused on personal productivity |
| Harvest | Easy time tracker, actionable reports, simple invoicing, wide integrations | Free solo version, Paid: $10.80/seat/mo | Capterra: 4.6/5, G2: 4.3/5 | Agencies needing easy time tracking and invoicing |
| Toggl Track | One-click tracking, project cost estimates, billable hour tracking, detailed reports | Free for up to 5 users, Paid: $9/user/mo | Capterra: 4.7/5, G2: 4.6/5 | Agencies wanting fast setup and clean tracking interface |
| Clockify | Automated timers, timesheets, team scheduling, project cost forecasting, reporting | Free forever plan, Paid: $3.99/user/mo | Capterra: 4.7/5, G2: 4.5/5 | Large teams needing basic tracking and flexible free plans |
| Timenotes | Editable time logs, team timesheets, client invoicing support, project management integrations | $39/year solo, $6.99/user/mo team plan | Capterra: 4.4/5, G2: Not listed | Small agencies needing basic tracking and invoicing |
| DeskTime | Automatic tracking, screen monitoring, project cost estimation, Pomodoro timer | Free for 1 user, Paid: $7/user/mo | Capterra: 4.5/5, G2: 4.6/5 | Agencies needing automatic tracking and activity monitoring |
Final thoughts
Choosing the right employee time tracking software for agencies is not just about managing hours; it’s also about optimizing productivity. It is about helping your team work smarter, improving project profitability, and building stronger client relationships.
You now know there are plenty of great tools out there, each offering its own strengths. But when you need employee time tracking that combines productivity analytics, payroll integration, attendance tracking, employee monitoring, and workforce management in one place, Time Doctor stands out.
Imagine what your agency could achieve if you had clear, real-time insights into where every hour goes.
What projects could you optimize?
Which clients could you serve better?
How much time and money could you save by avoiding hidden inefficiencies?
If your current system only tracks the basics, you may be missing out on improved performance, faster billing, and a more engaged team.
Are you ready to lead smarter, build a stronger team, and stop guessing where your agency’s time is really going?
Discover how Time Doctor can help you take full control of your agency’s time and productivity. Get a demo now.
Carlo Borja is the Content Marketing Manager of Time Doctor, a workforce analytics software for distributed teams. He is a remote work advocate, a father and an avid coffee drinker.