2025 Guide to Medicaid Billing for Special Education

If you were not satisfied with the Medicaid reimbursements your district received in 2023-2024, 2025 is the perfect time to consider learning more about Medicaid billing for special education—not just to comply with federal and state requirements, but also to provide your staff with peace of mind, avoid audits and penalties, and reclaim more funds for your district this year.

Embrace® has been supporting districts with Medicaid billing across five states for the past 20 years. Our EmbraceDS® Medicaid Billing software comes with personalized assistance from our Medicaid Success team, led by Stephanie Crouch.

Stephanie has nine years of Medicaid billing experience at Embrace® and oversees a team of five Medicaid specialists dedicated to helping districts maximize their reimbursements. In the 2023-2024 school year, her team successfully received over $89 million in reimbursements for Illinois districts!

Today, we sat down with Stephanie to ask her six key questions about Medicaid billing for special education in 2025.

How do we start Medicaid billing if we're new?

Starting Medicaid billing for a new public school district can be a complex process. Some states have unique billing systems or specific rules for school districts, so you'll need to familiarize yourself with the registration process specific to your state.

Basic steps may include enrolling, signing an Intergovernmental Agency Agreement (IGA)—which formalizes the relationship between the school district and your state’s Medicaid program—and establishing Medicaid billing protocols for your district.

Luckily, if you choose to become an EmbraceDS® customer, you won’t have to go through this process alone. Our Medicaid Success Team will assist you every step of the way.

How do we start Medicaid billing if we’re new?

Stephanie:

“Embrace® will work closely with your district to ensure registration is complete in all state-required systems for Medicaid billing.

Often, this includes one-on-one Zoom meetings to guide you through those systems together—something we're always happy to do. 

As we move through the registration process and Medicaid claims, our team will continue to provide ongoing support to ensure that you meet all state reporting deadlines.”

What training will be provided?

When you introduce new protocols, you'll need to ensure that your school’s administrative and health services teams are trained in Medicaid billing requirements. This includes understanding how to document services accurately, submit claims, and comply with state and federal regulations.

You will also need to find reliable software, like EmbraceDS®, that can simplify and streamline the entire billing process for your teams. Ideally, your Medicaid billing software should provide built-in tools to track services, create billing reports, and ensure compliance with state and federal rules.

As an EmbraceDS® customer, you'll receive both the software and a series of training sessions at no additional charge. You'll be assisted by Medicaid billing specialists who are familiar with your state’s procedures and regulations and have a proven track record of helping other districts in your state streamline their Medicaid billing.

What training will be provided?

Stephanie:

“Embrace® offers a 90-minute live webinar training for district providers—60 minutes of training with an additional 30 minutes allotted for questions.

Within the EmbraceDS® system, we also provide pre-recorded videos available at all times, including a full training that’s updated each year, as well as shorter videos for more specific guidance.

We also provide live annual refresher training, typically in the fall, for standard users, in addition to an admin training that reviews our reporting features.”

Who can use Medicaid billing software?

Once your school’s administrative and health services teams are trained in Medicaid billing requirements, they can begin documenting services and submitting claims. If you become an EmbraceDS® customer, all of your staff delivering medically necessary services will be able to use our software.

Additionally, the Embrace® Medicaid Success Team will be able to assist you and your team if any Medicaid billing questions arise, ensuring proper documentation and claim submission.

Who can use Medicaid billing software?

Should we only document services for Medicaid-eligible students?

After your registration and systems are set up, you can begin submitting claims for Medicaid reimbursement via your software provider.

EmbraceDS® allows you to keep detailed records of the services provided, the documentation supporting those services (e.g., IEPs, physician orders), and any other required paperwork for all students.

Should we only document services for Medicaid-eligible students?

Stephanie:

We encourage and recommend that providers document all services delivered to students who have an IEP, an IFSP, a 504 plan, or a health care plan, regardless of Medicaid eligibility status.

This is because students can fall in and out of Medicaid eligibility monthly. By documenting for all of these students, Embrace® can submit claims and capture additional reimbursement.”

How do we know if we're billing enough or missing reimbursement?

To ensure your district remains compliant and maximizes reimbursement opportunities, it’s important to stay on top of both prescribed and delivered services.

If you use EmbraceDS®, you'll gain access to multiple features that automatically report any discrepancies and save time for you and your team.

Stephanie:

One of the things Embrace® provides is a monthly accuracy report to our standard users and administrators.

EmbraceDS Accuracy Report

This report identifies any discrepancies between the service minutes that are prescribed in a student's plan, such as the health care plan, and the service minutes that were documented in EmbraceDS®.

We recommend that providers and administrators review these monthly as they become available. Another reporting feature we have is the EmbraceDS® dashboard, which I absolutely love.

EmbraceDS® Dashboard

The dashboard reflects multiple metrics related to errors for claims that we can't submit for reimbursement. There is a metric for each requirement the claim must meet for valid claim submission. By filtering out the claims that don’t meet state requirements, Embrace® keeps districts audit-ready at all times.

One of the main metrics is identifying users with billable claims that are not in the district’s Cost Pool for the current quarter. Identifying and reconciling any users who are not in the Cost Pool will assist the district in obtaining interim reimbursement. We recommend district administrators update this information in the state’s financial vendor’s program as soon as possible.

Another metric is the students with pending claims missing consent. This metric tells me that, for one or more students, the district has billable claims, but we can't submit them because there's a missing consent on file.”

What are the key points in Medicaid billing? How do we maximize reimbursement?

To maximize Medicaid reimbursements, it's important to keep your cost pools updated by ensuring that all Medicaid billing providers are correctly categorized. 

As an EmbraceDS® customer, you’ll be able to keep track of these metrics via our EmbraceDS® dashboard and reconcile any discrepancies in the data.

Stephanie:

“A couple of suggestions on how districts can improve their cost settlement and Medicaid allowable costs are ensuring districts are reporting accurate information in their state’s financial reporting program (such as PCG or Fairbanks) and that staff are responding to their Random Moment Time Study (RMTS) emails.

Our Embrace® Medicaid team supports districts with both of these processes, ensuring they are maximizing their reimbursement opportunities.”


If you don’t have internal expertise in Medicaid billing, you might want to consider working with a vendor like Embrace®, which can provide not only software but also personal assistance and help you manage the Medicaid billing process, reduce errors, and improve reimbursement rates.

Book the EmbraceDS® demo below!

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