How Congressional Budget Decisions Shape Rare Disease Funding—And What You Can Do

Congress is juggling three separate but intertwined legislative processes related to funding government operations, each of which have direct implications for the rare disease community: the Continuing Resolution, the Fiscal Year (FY) 2026 Appropriations Cycle, and Budget Reconciliation. The following brief overview is intended to help breakdown what is happening, what is at stake, and what can be done to support the resources and services that drive our rare disease research, therapy development, and access to care.

Continuing Resolution (CR) – Funding the government through the end of this fiscal year

President Trump has signed a Continuing Resolution (CR) that will fund the government through September 30. However, the bill includes cuts to critical programs, including reductions to the Department of Defense’s Congressionally Directed Medical Research Program and key health agencies such as the NIH and HRSA.

Unfortunately, the CR does not include language to reauthorize the Rare Pediatric Disease Priority Review Voucher (PRV) Program, which remains expired. This makes the push for reauthorization even more urgent. Both the House and Senate have introduced similar versions of the Give Kids a Chance Act, each proposing a five-year PRV extension.

A continuing resolution also means any funding increases or provisions included in the individual appropriations bills and “report language” will not be enacted, including language to establish a Rare Disease Interagency Coordinating Committee and supporting the innovative rare disease research at the National Center for Advancing Translational Sciences (NCATS). The House passed continuing resolution also did not include the reauthorization of the Rare Pediatric Disease Voucher Program. However, it did include an extension of Medicare telehealth flexibilities, ensuring continued availability of most telehealth services through September 30.

Action Opportunity: Use this action alert to contact your members of Congress about the importance of protecting funding for rare disease research and public health agency activities. The more Congress understands about how vital our federal infrastructure and services are for the rare disease community, the more champions for rare disease priorities emerge.

What’s Next – It’s time to plan for FY26

Once the FY2025 levels are set through the continuing resolution, Congress will immediately turn to the FY2026 appropriations cycle, which is expected to move quickly this year. For now, this will follow the typical cycle for appropriations. Members of Congress seek input on community priorities from advocates and the Appropriations Committees develop the 12 pieces of legislation that will set funding levels and convey their priorities for federal agencies to address over the next year. This starts on October 1, 2025.

The Wildcard – Budget Reconciliation

This year, Congress is expected to go through an additional process related to government funding called budget reconciliation. It includes two parts – a budget resolution with instructions on federal spending amounts and an expedited process to pass related legislation. To be included in budget reconciliation, a policy has to have a direct impact on federal spending, but the resulting legislation can be passed in the Senate with 51 votes instead of 60.

On February 25, the House passed their version of a budget resolution, including reconciliation instructions that require $1.5 billion in spending cuts, including a $880 billion cut from the committee that oversees Medicare, Medicaid, and other health programs. The Senate must agree to the same framework, or they will pass their own version and seek to work with the House on a compromise. If they do, then Congress will begin determining what spending cuts and other eligible policy to include.

Action Opportunity: The House budget resolution has sparked real concern about the future of Medicaid funding. Please know that Congress still has a lot of work to do before anything is finalized. But if the required cuts in the House version are enacted, it will be challenging to achieve the required spending cuts without making significant changes to Medicaid funding. Medicaid is a critical safeguard for our rare disease community through traditional eligibility routes and waiver programs that enable coverage for children’s complex health needs.

Now more than ever, Congress should understand why Medicaid matters to rare disease patients and families. Use this action alert to share with your member of Congress why Medicaid is critical to our community, so they understand the impact of having insurance coverage as they consider policy options in the coming months.

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EveryLife Foundation for Rare Diseases is a nonprofit, nonpartisan organization dedicated to advancing the development of treatment and diagnostic opportunities for rare disease patients through science-driven public policy. The Foundation works to improve the lives of the millions of Americans suffering from rare diseases by advocating for policies that foster innovation and remove barriers to life-saving treatments. To learn more, visit EveryLifeFoundation.org.