All Collections
HRA Reimbursement FAQs
Administrator Reimbursement FAQs
How do I reimburse my employees through payroll?
How do I reimburse my employees through payroll?

How do I get the funds to my employees tax-free?

Support avatar
Written by Support
Updated over a week ago

As the business owner or plan administrator, you have some options and get to make the choice! Remember, the tax-free nature of the QSEHRA or ICHRA comes from having your plan documents in place, staying compliant, and having the proper year-end W-2 reporting. With our HRA platform at Take Command Health, we'll take care of that part for you. We'll track your employees' claims, and then each month, we'll deliver a Reimbursement Statement so you know exactly how much to reimburse your employee.

Getting your employees the money is the final part. Here are some of the common reimbursement methods we see:

  1. Reimburse through your payroll system (recommended)

  2. Write a check

  3. Pay cash

  4. Use Paypal or another transfer service

In this article, we'll explain how to setup and make HRA reimbursements through your payroll system. We recommend reimbursing through payroll because it makes it easy to track reimbursements, will direct deposit into your employees' accounts (assuming they have that set up), and can roll-forward automatically each month to make your job, as the administrator, much easier.

General Instructions for HRA and Payroll

Depending on the payroll provider you use, you may need to talk with your payroll administrator to help. In general though, we have some directions to help you.


Because these payments aren't taxable, they don't appear on payroll tax or other tax reports. 

Remember, what goes on the W-2 for QSEHRA is the amount offered and not the amount claimed. This goes on Box 12, Code FF.  There are no specific tax reporting requirements for ICHRA.

To set up tax-free reimbursements:

  1. Open or edit your employee's pay template 

  2. Add a recurring, non-taxable expense or reimbursement-type

  3. Enter the amount provided on the Reimbursement Statement from Take Command Health

  4. Save or schedule for the next pay run

Most payroll systems will carry that amount forward each month. For example, if you added a $200/mo reimbursement for an employee, the recurring settings should carry that forward so that the employee will get the same $200/mo until changed. That means you'll only need to make adjustments when there is a change. This makes it super easy for premium-only HRAs, as the amounts will not change very often and can roll forward. For HRAs that include medical expenses, you'll need to make a quick edit each month beforehand if the amount is different. To help, you can choose the day of the month you'd like Take Command Health to deliver the Reimbursement Statement so that you have time to make these changes before a pay run (In the admin settings, under Reimbursements, you can change the day of the month for the Reimbursement Statement).


While most reimbursements through QSEHRA are tax-free, there are a few types of allowable reimbursements that must be taxed. 

Taxable reimbursements are reported as income and taxed like regular Wages with income & payroll taxes withheld. You can usually enter this as an "Additional Income" or "Other Earnings" line item, but check with your payroll company on the best way to categorize it.

The only taxable reimbursements through QSEHRA include premiums paid pre-tax through a spouse's employer for a group plan.

You can choose whether or not to allow for these taxable reimbursements through your QSEHRA- if you're not sure if you allow these or not, just reach out to us and we can let you know!

End of Year W-2 Reporting (QSEHRA Only)

Although that takes care of the month-to-month reimbursements, you'll want to be aware of year-end requirements too. QSEHRA offerings have to be reported on each employee's W2 form in Box 12 with code FF. Not a big deal now, but you'll want to talk with your CPA or payroll admin to figure out how to add that amount. Some payroll systems have codes you can use to do it automatically, some may require manual edits. 

Specific Providers

Ok, so those are the general instructions that should work for most payroll providers (again, you may need to ask someone at the payroll firm you use to help or share these instructions). If you use Gusto, Zenefits, or Quickbooks/Intuit Payroll, we have specific instructions to help you get started!

Did this answer your question?