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Medicaid & Medicare

New York Medicaid Timely Filing for Therapists: What to Know

New York Medicaid timely filing for therapists and psychiatrists comes down to one number for fee-for-service claims: 90 days from the date of service. Timely Filing means sending a clean claim before the payer’s deadline. This guide covers the state rule, the delay reasons that can save a late claim, and what managed care plans say.

New York Medicaid timely filing for therapists: a biller checking claim dates on a calendar
Count the days from the date of service.

What is the New York Medicaid 90-day rule?

The 90-day rule says a New York Medicaid claim must be initially submitted within 90 days of the date of service. The state’s Guide to Timely Billing (August 9, 2018) cites 18 NYCRR 540.6(a) for this. A claim sent later needs a valid delay reason. Without one, it denies.

Medicaid fee-for-service rules

New York Medicaid timely filing for therapists under fee-for-service follows the state manual.

Fee-for-service means New York Medicaid pays the claim directly, through eMedNY, the state’s Medicaid billing system. The General Billing manual (version 2025-1, June 9, 2025) sets out the rules below. The New York State Department of Health runs the program.

Delay reasons

A delay reason is a numeric code you attach to a claim older than 90 days. The manual lists codes 1 through 11 and 15, and the state does not accept exception requests outside them. A few examples:

  • Code 1: proof of eligibility unknown or unavailable. Submit within 30 days of eligibility notification.
  • Code 7: third-party processing delay. Submit within 30 days. Paper claims need the other payer’s Explanation of Medical Benefits.
  • Code 9: the original claim was rejected or denied for a reason unrelated to timeliness. Resubmit within 60 days.

Pick the code that matches what happened, because New York Medicaid timely filing for therapists depends on a documented reason. Keep your documentation on file.

Corrections and the two-year limit

Corrected or resubmitted claims generally must go back within 60 days of notification. A Corrected Claim that replaces a paid claim keeps the original claim number. A void starts over as a new claim, so timeliness edits apply again. Separately, claims must be payable within two years of the date of service. The manual says the state considers older claims only with documentation of agency error or a court order.

New York Medicaid timely filing for therapists in managed care

Medicaid managed care means a private plan under state contract pays the claim, so the plan sets its own filing limit in your contract. We read one plan’s policy. The Anthem Blue Cross and Blue Shield New York Medicaid timely filing policy, effective June 3, 2025, lists 90 days for participating providers and 15 months for nonparticipating providers. Other plans may differ. Read each plan’s policy and your contract.

Where do behavioral health claims fit?

The General Billing manual has no text on behavioral health, so use it as the baseline for claims paid directly by the state. For any behavioral health rule, check the manual for your service or ask the Department of Health. Do not assume a managed care plan follows the same clock.

What to do Monday morning

  1. Run an aging report on unpaid New York Medicaid claims and flag anything near 90 days.
  2. Split the list into fee-for-service and each managed care plan.
  3. Check each claim’s rejection history. A denial unrelated to timeliness may qualify for delay code 9.
  4. Save every Clearinghouse acceptance report as proof of the original filing date.
  5. Look up each plan’s current filing limit in its own policy.

This post covers New York Medicaid timely filing for therapists only. Medicare and commercial plans have separate deadlines. For Medicare, see our Medicare timely filing guide.

Related guides

Compare how another state handles deadlines in our MassHealth timely filing and appeals guide. Our state billing guides, Resources hub and insurance companies contact directory can help you find the right payer. Our Who We Serve page shows the practices we work with.

The short version: new york medicaid timely filing for therapists

For New York Medicaid timely filing for therapists, send fee-for-service claims within 90 days of the date of service. If you are late, use the delay reason that fits and keep proof. For managed care, read the plan’s own filing limit.

How MCM South helps

MCM South Medical Billing Service bills for psychotherapists and psychiatrists in solo and medium-size practices. We watch claim dates and rejections so deadlines do not slip past you.

Sources checked (November 4, 2026)

Keep going

Related reading

  1. MassHealth Timely Filing and Appeals for Therapists and Psychiatrists
  2. Medicare Timely Filing for Therapists: What the 12-Month Rule Means
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Frequently asked questions

What is the New York Medicaid timely filing limit?

Fee-for-service claims must be initially submitted within 90 days of the date of service. The eMedNY General Billing manual (version 2025-1) states this. Later claims need a valid delay reason code.

What if I miss the 90 days?

Attach the delay reason that matches your situation and keep the documentation. The eMedNY guide lists codes such as 1 for unknown eligibility and 9 for an earlier denial unrelated to timeliness. Each has its own 30- or 60-day window.

Is there a final deadline for New York Medicaid claims?

Yes. Claims must be payable within two years of the date the care was furnished. The manual says the state considers older claims only with documentation of agency error or a court order.

Do Medicaid managed care plans use the same 90 days?

Not necessarily. Anthem’s New York Medicaid policy lists 90 days for participating and 15 months for nonparticipating providers. Other plans set their own limits, so read each plan’s policy.

Where MCM South works

MCM South works only in mental and behavioral health. We serve psychotherapists and psychiatrists in solo and medium-size practices across ten currently served states: Georgia, Massachusetts, Connecticut, Texas, Florida, New York, Colorado, Tennessee, North Carolina and Illinois. Need a payer contact? Use our insurance companies contact directory.