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The Best Payroll Software for Education in 2023

Whether you are looking for an all-in-one solution or something more specific, here are the best payroll software options for educational institutions in 2023. Get a clear overview of the features and benefits of each to make the best choice for your organization.

Schools and universities require payroll software that can handle a variety of HR functions, including time tracking, tax filing, employee self-service and more. The top payroll software for schools and universities offers all these features, reliable customer support and a well-designed user interface to help streamline payroll processing. We have compiled and compared the best payroll solutions for the education industry. On this page, you will also find tips on choosing the best payroll software for your educational institution and some top features to consider in your search.

Top payroll software for schools and universities

This table offers a quick comparison of the core features offered by the top payroll software for schools and universities.

Native time tracking Free trial Employee self-service Tax filing Mobile app Pricing (per month)
Zoho Payroll Yes Yes Yes Yes Yes $19 fixed plus $3 per employee
Gusto Yes Yes Yes Yes No $40 fixed plus $6 per employee
Papaya Global Yes No Yes Yes Yes $12 per employee
OnPay No Yes Yes Yes Yes $40 fixed plus $6 per employee
Wave Yes Yes Yes No No $35 fixed $6 per employee
QuickBooks Payroll Add-on Yes Yes No No $37.50 per month + $5 per employee.

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Zoho Payroll: Best for simple payroll processing

Image: Zoho

As a top choice for payroll solutions for schools and universities, Zoho Payroll offers a variety of features to simplify payroll processing. It can automatically calculate employee payroll, automate pay schedules, deduct taxes and approve pay runs. While Zoho payroll helps empower schools and universities, it also helps makes it easier for employees through its employee self-service portal.


  • Predefined employee benefits: You get a list of predefined employee benefits, including retirement plans, 401(k) and health insurance.
  • Pay out unused leave: Depending on your school or university policies, you can use Zoho payroll to pay out unused leaves to reward your diligent employees.


  • Simple and easy to use.
  • Advanced time tracking tools.
  • Deep integration with Zoho People.


  • Customer support is not the best.
  • Mobile app interface needs improvement.


  • $19 fixed plus $3 per employee.

Gusto: Best for scalability

Image: Gusto

Gusto’s scalability makes it work for schools and universities of all sizes. This full-service payroll platform is cloud-based, making it easy to scale up or down. Gusto payroll also offers integrations with third-party business software to extend HR functionality and customize the system further. Along with the core payroll features, Gusto offers advanced tools such as paid time off management.


  • Gusto Wallet: This is a unique feature offered by Gusto to help users save from each paycheck and keep track of their spending.
  • Tiime-saving automation: You can set up Gusto payroll to automatically calculate and deduct taxes and run payroll for you. It can even automatically complete new hire reporting duties.


  • Variety of HR add-ons available.
  • Integration with a wide range of applications.
  • Multiple paid plans.


  • No mobile app.
  • Entry-level plan is too basic and missing some core features.


  • Simple: $40 fixed plus $6 per employee.
  • Plus: $60 fixed plus $9 per employee.
  • Premium: Customized pricing.

Papaya Global: Best for international payroll

Image: Papaya Global

Papaya Global is the best payroll software for a global workforce. If you have staff or teachers outside the United States, you can use Papaya Global to process payroll and make payments. Papaya Global offers its payroll services for over 160 countries. It also consolidates data streams and automates workflows to provide all the information on a centralized platform.


  • Employee of record: The EOR function allows schools and universities to handle payroll in a foreign country without setting up a local entity.
  • Local compliance: Papaya Global offers a team of compliance experts to simplify international payroll.


  • Customized plans.
  • Global coverage.
  • Robust reporting and analytics.


  • Initial setup is time-consuming.
  • Customized plans are expensive.


  • Full-service payroll: Prices start at $12 per month per employee.
  • Global Expertise Services: $250 per month per employee.
  • Employer of Record: $770 per month per employee.

OnPay: Best for a small school or university

Image: OnPay

OnPay is an easy-to-use payroll processing platform. There is only one plan that includes all the features, such as an employee self-service portal, tax filing and unlimited payroll runs. The simple interface, affordable price point and single plan make OnPay ideal for small organizations. Time tracking is unavailable but can be added through third-party integration.


  • Payroll flexibility: You get flexibility in how you want to pay the employees, including an option to pay via prepaid debit cards. You can also choose pay-as-you-go workers’ compensation to avoid large payments upfront.
  • Ease of use: OnPay has a straightforward and clean interface, making it easy to navigate. Each employee has a user dashboard that includes details about past and upcoming pay runs, deductions and more.


  • Unlimited payroll runs.
  • Extensive list of third-party integrations.


  • No native time tracking.
  • Payroll approval feature is not fully automated.


  • $40 fixed plus $6 per employee per month.

For more information, read the full OnPay review.

Wave: Best for seasonal workers

Image: Wave

Wave payroll is an add-on to the full Wave HR suite, which includes account and invoicing features. The payroll features of Wave are highly customizable, so schools and universities can configure the system according to their needs. It is extremely easy to manage employee rosters, making Wave payroll ideal for organizations with evolving staff needs or seasonal workers.


  • Auto Sync with Wave Accounting: All payroll related expenses from Wave Payroll  automatically sync with Wave Accounting general ledger. You also get automatic journal entries on the Transactions page.
  • Timesheets: You can use this feature to track hours of your school or university staff, including salaried and hourly employees.


  • Syncing with other Wave applications.
  • Easy management of employee rosters.


  • Tax filing is not available in all U.S. states.
  • No mobile app.


  • With tax filing: Base fee of $35 plus $6 per employee per month.
  • Without tax filing: Base fee of $20 plus $6 per employee per month.

QuickBooks Payroll: Best for users of QuickBooks accounting

Image: QuickBooks

QuickBooks payroll is a subscription to the full QuickBooks software. You can choose from three different plans depending on your needs. If your school or university is already using QuickBooks, this would easily be the best payroll solution for you. Some of the top payroll features of QuickBooks include direct deposits, unlimited payroll runs and customizable payroll reports.


  • Tax penalty protection: With the Elite plan, you get tax penalty protection for up to $250,000 annually. This means if there are any errors in tax filing, QuickBooks will cover any penalties associated with the error.
  • Fast direct deposit: With QuickBooks Payroll, you get same-day or next-day direct deposit. The same-day deposit is available in the Premium and Elite plan.


  • Robust reporting and analytics.

  • Wage garnishment feature.
  • Deep integration with QuickBooks applications.


  • Time tracking and 24/7 support are not available in the Core plan.
  • Limited integrations.


  • Core: $37.50 per month + $5 per month per employee.
  • Premium: $50 per month + $5 per employee.
  • Elite: $80 per month + $8 per employee.

For more information, read the full QuickBooks review.

Key features of payroll software for schools and universities

Employee self-service

School and university staff and teachers need access to their digital payslips and tax information. Having an employee service portal helps reduce the burden on HR staff, as employees are empowered to complete such tasks themselves.

Tax filing

The year-end tax computations for schools and universities can get quite complex. With an automatic tax filing feature, payroll solutions can help streamline the entire process.

Native time tracking

While third-party integration for time tracking is available with most payroll software, having native capabilities help provide a seamless experience. Time tracking helps school or university administration manage payroll based on attendance, paid time-off, sick days and mandatory leaves.

Mobile app

A mobile app for payroll software allows users to complete and manage tasks while away from a computer. For example, they can use the mobile app to document time tracking or to approve timesheets.

Free trial

The primary advantage of a free trial is that it offers an opportunity for users to get a feel for the payroll software, such as with the user interface and core features. They can use the free trial to decide whether to adopt the software at their educational institution.

How do I choose the best payroll software for school and university?

When choosing the best payroll software for your school or university, you need to start with a self-analysis to determine what problems or challenges you want to fix with the software. Each payroll software offers pros and cons, so you must dig deeper through demo sessions or a free trial to truly understand which software suits your needs. For example, if you anticipate needing to scale up operations at your school or university, it is best to use flexible cloud-based software so you don’t have to set up a new payroll system every few years.

SEE: Choosing a payroll service: A guide for business leaders (TechRepublic Premium)

A good payroll software will minimize the workload of your school and university staff by using software automation tools to minimize redundant or recurring payroll-related tasks. This enables teachers to focus on their students and not worry about issues with their salary. An efficient payroll management system will make the lives of your accountants, HR staff, teachers, and school finance officers much easier. It will also help to make a budget for purchasing payroll software. Choosing the right payroll software for your institution also depends on if you want the application to integrate with your existing tech stack at your school or university. Most organizations want to streamline their operations by integrating their tech stack as it makes managing payroll software more efficient.


We explored dozens of payroll software to find the best solutions for schools and universities. We found software that offers flexibility and scalability ideal for educational institutes. Several other parameters were also considered, including pricing, user interface, customer support and the availability of important features such as time tracking, third-party integrations and employee self-service tools.

Read next:  8 best enterprise accounting software for 2023

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