Updated May 2026 · Florida Plan Finder · Licensed Florida Health Insurance Producer

Setting Up Payroll for the First Time at a Physical Therapy Clinic in Jacksonville, FL

The first hire at a Jacksonville physical therapy clinic — usually a part-time PTA or front-desk coordinator — triggers a dozen one-time setup steps that most clinic owners do badly because they only do them once. Done wrong, you're looking at IRS notices, Florida Department of Revenue inquiries, and back tax assessments six months in. Done right, you have a system that handles every future hire automatically. This page is the practical setup checklist for a Duval County PT clinic.

Step 1: Federal Employer Identification Number (EIN)

If the clinic doesn't already have an EIN (S-corps and LLCs typically do; sole proprietors often don't), get one immediately. Apply at irs.gov/ein. Application takes 10 minutes; EIN is issued instantly. Free.

The EIN goes on Form W-2, payroll tax filings, workers' comp applications, and the new-hire packet. Keep it in your password manager.

Step 2: Florida Reemployment Tax Registration

Florida's unemployment insurance tax is called "reemployment tax." Register with the Florida Department of Revenue at floridarevenue.com via Form DR-1 (Registration). For a new employer:

• Initial rate: 2.7% of the first $7,000 of each employee's wages annually
• Tax base: first $7,000/year per employee — maximum tax per employee is $189/year
• After 6+ quarters of experience, rate adjusts based on the clinic's claims history (can drop as low as 0.1% with no claims)

Reemployment tax is filed quarterly on Form RT-6. Most payroll services file it automatically.

Step 3: Florida New Hire Reporting

Florida requires reporting new hires within 20 days at servicesforemployers.floridarevenue.com. Information needed: employee name, SSN, address, hire date, employer EIN. This feeds the state child support enforcement system. Free, takes 5 minutes per hire.

Most payroll services handle this automatically once you provide the new hire information through their onboarding flow.

Step 4: Workers' Compensation Insurance

Florida requires workers' comp for non-construction businesses with 4+ employees. Until the clinic has 4 employees, workers' comp is optional but strongly recommended (a single PT injury during patient transfer can be a $20K+ claim). For PT clinics:

• Class code 8829 (chiropractic, PT, occupational therapy office) typically rated $0.85–$1.25 per $100 of payroll
• For a clinic with $200K of W-2 payroll, premium runs roughly $1,700–$2,500/year
• Buy through any Florida-licensed agent; pay-as-you-go options available

Step 5: Choose a Payroll Service

For a 1–10 employee Jacksonville PT clinic, the practical options:

For a small PT clinic, Gusto and QuickBooks Online Payroll are the most common picks. Both handle federal/state filings, W-2/1099 generation, direct deposit, and benefits integration.

Step 6: Withholding Setup for Each Employee

Each employee completes:

• Form W-4 (federal income tax withholding): Employee specifies filing status, dependents, and any additional withholding
• Form I-9 (employment eligibility verification): Federal requirement; clinic verifies identity and work authorization documents
• Direct deposit authorization: Voided check or bank-provided routing and account info
• Florida new hire reporting (clinic's responsibility, not employee's)

Florida has no state income tax — no state W-4 is needed.

Step 7: Set Up Quarterly Federal Filings

The federal payroll filings the clinic must handle (or have its payroll service handle):

• Form 941 (quarterly): Federal income tax withheld + employer/employee FICA. Due April 30, July 31, October 31, January 31
• Form 940 (annual): FUTA tax. Due January 31
• Form W-2 / W-3 (annual): Wage statements to employees and SSA. Due January 31
• Federal tax deposits: Generally semi-weekly or monthly via EFTPS, depending on tax liability size

Step 8: Florida Quarterly Filings

• Form RT-6 (Reemployment Tax): Quarterly. Due same dates as federal 941.
• Workers' comp audits: Annual at policy anniversary. Provide payroll records for actual-vs.-estimated reconciliation.

Step 9: Benefits and Voluntary Deductions

Once the basic payroll is running, layer on:

• Health insurance pre-tax employee contribution (Section 125 cafeteria plan)
• Retirement plan contributions (SIMPLE IRA, 401(k))
• HSA contributions (if HDHP)
• Garnishments (when applicable)

Step 10: Recordkeeping

Federal record retention requirements for the clinic:

• Form I-9: longer of 3 years from hire OR 1 year from termination
• Payroll records (W-2, time records, pay stubs): 4 years (FLSA), 6 years (state best practice)
• Form 941 and 940 returns: 4 years
• W-4s: 4 years after the last return that used them

Common First-Payroll Mistakes

• Skipping reemployment tax registration: Florida DOR sends a notice within 60 days. Penalties are modest if fixed quickly.
• Treating the first employee as 1099: Almost always wrong for a PT clinic hire. Set up payroll properly from day 1.
• Underwithholding federal tax: Use the W-4 calculator the IRS provides. Employees with multiple jobs or working spouses often need more withholding than the default.
• Missing the Form I-9 deadline: Must be completed within 3 business days of hire. Audits can fine $250–$2,500 per missing/late I-9.
• Forgetting workers' comp before hire #4: The 4-employee threshold can be crossed without realizing it. Each part-time hire counts.

Frequently Asked Questions