The IRS requires Nebraska employers to make federal payroll tax deposits through EFTPS (Electronic Federal Tax Payment System) — missing a deadline by even one day triggers penalties. As a Nebraska employer, you have federal deposits via EFTPS and separate state withholding deposits through NDOR. This guide covers everything you need to know.

What Is EFTPS?

EFTPS (Electronic Federal Tax Payment System) is the IRS's free online portal at eftps.gov for making federal tax payments. It is the required channel for federal payroll tax deposits — no paper check alternative exists for most employers. Federal taxes deposited through EFTPS include: employee income tax withholding, Social Security (6.2% + 6.2%), Medicare (1.45% + 1.45%), Additional Medicare Tax, and FUTA (Form 940).

How to Enroll in EFTPS

  1. Go to eftps.gov and click Enrollment, then select Business.
  2. Enter your EIN, business name, address, and bank account/routing number.
  3. Submit. The IRS mails a PIN to your business address within 5–7 business days.
  4. When the PIN arrives, return to eftps.gov, enter the PIN, and create a password.
  5. Your account is now active. Enroll immediately after getting your EIN — not when a payment is due.

Monthly vs. Semi-Weekly Depositors

Schedule Lookback Liability When to Deposit
Monthly≤ $50,000By 15th of following month
Semi-weekly> $50,000Within 3 business days of payday
New employersN/AMonthly for first calendar year

The IRS Lookback Period

Your deposit schedule is determined by total Form 941 tax liability during the 12-month lookback period ending June 30 of the prior year. For 2026: July 1, 2024 – June 30, 2025. Add line 12 of Form 941 for Q3 2024, Q4 2024, Q1 2025, and Q2 2025. Total ≤ $50,000 = monthly. Total > $50,000 = semi-weekly. Your schedule is locked for the entire calendar year.

The $100,000 Next-Day Deposit Rule

If your accumulated undeposited tax liability reaches $100,000 on any single day, you must deposit it by the next business day regardless of your assigned schedule. Monthly depositors who trigger this rule are automatically converted to semi-weekly for the rest of that year and all of the next year.

How to Make a Payment in EFTPS

  1. Log in at eftps.gov with your EIN and password.
  2. Click Make a Payment and select the tax form (941 for payroll, 940 for FUTA).
  3. Select the tax period and enter the payment amount.
  4. Set the payment date — must be at least one business day before the due date.
  5. Confirm and save the confirmation number.

Penalties for Late EFTPS Deposits

Days Late Penalty
1–5 days2%
6–15 days5%
More than 15 days10%
After IRS notice15%

The IRS First Time Penalty Abatement (FTA) program can waive the first late-deposit penalty if you have a clean compliance history. Call the IRS and request abatement.

Nebraska State Withholding Deposits: Separate from EFTPS

EFTPS only covers federal taxes. As a Nebraska employer, you have a second deposit obligation: state income tax withholding must be submitted to the Nebraska Department of Revenue (NDOR) at revenue.nebraska.gov. The deposit schedule and payment portal are entirely separate from EFTPS. Most Nebraska employers deposit state withholding monthly or quarterly depending on their withholding volume. Check NDOR directly for current thresholds and due dates.

Failing to deposit Nebraska state withholding on time triggers separate state penalties on top of any IRS penalties for missed federal deposits. A payroll service handles both automatically.

Let Payroll Software Handle EFTPS for You

Gusto automatically calculates your payroll taxes and makes federal and Nebraska state deposits on time — every time. No manual EFTPS entries, no penalty risk.

Try Gusto Free →

Payroll software like Gusto handles the entire deposit workflow automatically: it calculates taxes after each payroll, schedules the EFTPS payment for the correct due date, and keeps your deposit schedule synced with the lookback period. Most Nebraska small business owners who start doing payroll manually eventually switch after missing one deadline and paying a penalty.