Home Health Agencies: Payroll Setup Guide (2026)

Setting up or managing payroll for home health agencies involves more steps than the basic payroll guides cover. DOL live-in caregiver regulations, Medicaid waiver payroll requirements, state home health aide certification records applies on top of standard federal requirements.

This guide covers the specific payroll setup and management requirements for home health agencies.

Step 1: Get Your Employer Accounts Set Up

Before running payroll for home health agencies, you need an Employer Identification Number (EIN) from the IRS, a state employer withholding account in each state where you have employees, and a state unemployment insurance (SUTA) account. For home health agencies operating in multiple states, this means separate registrations in each state.

Step 2: Configure Pay Types for Home Health Agencies

Home Health Agencies have non-standard pay types that require specific configuration: visit-based aide pay, travel time reimbursement, Medicaid billing vs payroll, live-in caregiver rules. Each of these must be set up as a separate pay code in your payroll system with the correct tax treatment applied.

Missing this step means your system calculates overtime incorrectly, applies the wrong withholding rate, or misses required reporting -- and you do not find out until you receive a penalty notice or employee complaint.

Step 3: Set Up Compliance Tracking

Home Health Agencies payroll compliance requires: DOL live-in caregiver regulations, Medicaid waiver payroll requirements, state home health aide certification records. Each of these has filing deadlines, rate requirements, or calculation rules that must be maintained current.

Set up a compliance calendar that tracks: tax deposit deadlines (semi-weekly or monthly based on your lookback period), quarterly Form 941 due dates, annual Form 940 due dates, state quarterly filings, and new hire reporting requirements.

Step 4: Run Payroll and File on Time

With accounts set up and pay types configured, run payroll on your selected frequency. For home health agencies, bi-weekly or semi-monthly works for most salaried staff. visit-based aide pay may require different frequency or supplemental runs.

Tax deposits must be made on the IRS schedule -- either semi-weekly (if your lookback period tax liability exceeds $50,000) or monthly (if less than $50,000). Missing the deposit date triggers the IRS failure-to-deposit penalty.

The Faster Path: Managed Payroll for Home Health Agencies

BEG managed payroll handles all of the above for home health agencies at $25-$45 PEPM, all-inclusive. Setup takes 3-5 business days. We configure your pay types, establish your tax accounts, and run your first payroll on schedule.

Frequently Asked Questions