Best Payroll Software for Education in 2023

Goff Justice announces a $20 million expansion of nursing education programs

Whether you are looking for a comprehensive solution or something more specific, here are the best payroll software options for educational organizations 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 best payroll software for schools and universities offers all of these features, reliable customer support, and a well-designed user interface to help simplify payroll processing. We’ve 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 important features to consider in your search.

The best payroll software for schools and universities

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

Track the original time Free trial Employee self service Tax declaration mobile application Pricing (per month)
ZohoPayroll Yes Yes Yes Yes Yes $19 flat plus $3 per employee
Mile Yes Yes Yes Yes no $40 flat plus $6 per employee
Papaya Global Yes no Yes Yes Yes $12 per employee
OnPay no Yes Yes Yes Yes $40 flat plus $6 per employee
Wave Yes Yes Yes no no $35 flat $6 per employee
QuickBooks Payroll addition Yes Yes no no $37.50 per month + $5 per employee.

jump to:

Zoho Payroll: Best for simple payroll processing

Image: Zoho

As the 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 salaries, automate pay schedules, deduct taxes and approve payments. While Zoho Payroll helps empower schools and universities, it also helps make it easier for employees with 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 Unused Vacation: Depending on your school or university’s policies, you can use Zoho Payroll to pay for unused vacation to reward your hardworking employees.


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


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


  • $19 flat plus $3 per employee.

Gusto: Best for scalability

Photo: 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 further customize the system. Besides the basic payroll features, Gusto offers advanced tools like managing paid time off.


  • Gusto Wallet: This is a unique feature offered by Gusto to help users save from every paycheck and keep track of their spending.
  • Automate Tiime Provisioning: You can set up Gusto Payroll to automatically calculate and deduct taxes and run the payroll for you. It can also automatically complete new hire reporting duties.


  • A variety of HR add-ins are available.
  • Integration with a wide range of applications.
  • Multiple paid plans.


  • There is no mobile app.
  • The entry level plan is very basic and is missing some essential features.


  • Simple: $40 flat plus $6 per employee.
  • Plus: $60 flat plus $9 per employee.
  • Premium: Custom pricing.

Papaya Global: Best in International Payroll

Photo: Papaya Global

Papaya Global is the best payroll software for the global workforce. If you have employees or teachers outside the United States, you can use Papaya Global to process payroll and make payments. Papaya Global provides payroll services to more than 160 countries. It also integrates data flows and automates workflows to provide all information on a centralized platform.


  • Registered Employee: The EOR functionality allows schools and universities to handle payroll in a foreign country without setting up a local entity.
  • Domestic Compliance: Papaya Global offers a team of compliance experts to streamline international payroll.


  • custom plans.
  • Global coverage.
  • Powerful reports and analytics.


  • The initial setup takes a long time.
  • Dedicated plans are expensive.


  • Full Service Payroll: Prices start at $12 per month, per employee.
  • Global Experience Services: $250 per month, per employee.
  • Registered employer: $770 per month, per employee.

OnPay: Best for a small school or university


OnPay is an easy-to-use payroll processing platform. There’s just one plan that includes all the features, such as an employee self-service portal, tax filing, and unlimited payroll running. The simple interface, reasonable price point, and individual plan make OnPay ideal for small businesses. Time tracking is not available but can be added through third party integration.


  • Payroll flexibility: Gain flexibility in how you want to pay employees, including the option to pay via prepaid debit cards. You can also choose workers compensation on a pay-as-you-go basis to avoid large payments up front.
  • Ease of Use: OnPay has a clear and clean interface, making it easy to navigate. Each employee has a user dashboard that includes details about past and upcoming payments, discounts, and more.


  • Run unlimited payroll.
  • Extensive list of third party integrations.


  • Do not follow the original time.
  • The payroll approval feature is not fully automated.


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

For more information, read our full OnPay review.

Wave: Best for seasonal workers

Photo: The Wave

Wave Payroll is an addition to the full Wave HR suite, which includes calculation and billing features. Wave’s payroll features are highly customizable, so schools and universities can configure the system according to their needs. Employee rosters are incredibly easy to manage, making Wave Payroll ideal for organizations with evolving employee needs or seasonal workers.


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


  • Sync with other Wave apps.
  • Easy management of employee lists.


  • Tax filing is not available in all US states.
  • There is no mobile app.


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

QuickBooks Payroll: Best for QuickBooks Accounting users

Image: Quickbooks

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


  • Protection from tax penalties: With the elite plan, you get up to $250,000 in tax protection annually. This means that if there are any errors in your tax filing, QuickBooks will cover any penalties associated with the error.
  • Fast Direct Deposit: With QuickBooks Payroll, you can get a same-day or next-day direct deposit. Same day deposit is available on the Premium and Elite plans.


  • Powerful reports and analytics.

  • Pay booking feature.
  • Deep integration with QuickBooks applications.


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


  • Basic: $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 our full QuickBooks review.

Key features of payroll software for schools and universities

Employee self service

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

Tax declaration

Year-end tax calculations for schools and universities can get quite complicated. With the automatic tax filing feature, payroll solutions can help streamline the entire process.

Track the original time

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

mobile application

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

Free trial

The primary advantage of a free trial is that it provides an opportunity for users to get familiar with the payroll software, such as its user interface and basic features. They can use the free trial to decide whether to adopt the software in 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 should start with a self-analysis to identify the problems or challenges you want to fix with the software. Each payroll program offers its pros and cons, so you should dig deeper into trial sessions or a free trial to understand which program really suits your needs. For example, if you anticipate the need to scale operations at your school or university, it’s best to use flexible cloud software so you don’t have to set up a new payroll system every few years.

be seen: Choosing a Payroll Service: A Guide for Business Leaders (TechRepublic Premium)

A good payroll software will reduce the workload of your school and university staff by using software automation tools to reduce redundant or redundant payroll related tasks. This allows teachers to focus on their students and not worry about their pay issues. An effective payroll management system will make the lives of accountants, HR staff, teachers, and school finance officers much easier. It will also help budget for the purchase of payroll software. Choosing the right payroll software for your organization also depends on whether you want the app to integrate with your existing school or university tech stack. Most organizations want to streamline their operations by integrating their suite of technologies as it makes managing payroll software more efficient.


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

read the following: 8 best corporate accounting software for 2023