While President Donald Trump’s “One Big Beautiful Bill” did a whole lot the healthcare sector opposes, it also failed to deal with a plethora of more mundane health legislation lawmakers must finalize as soon as this fall.

Authorizations or funding for matters such as community health centers, telehealth and hospital-at-home are due to expire when the fiscal year ends Sept. 30 or when the calendar year ends. The latter category includes enhanced subsidies for health insurance exchange plans.

These include legislation targeting prior authorization and pharmacy benefit manager business practices. One issue that nearly made it into the tax package is cracking down on Medicare Advantage “upcoding,” a priority for a growing number of Republicans.

There is no deadline for these bills, and the thorny issues of extending exchange subsidies and preventing Medicare cuts could theoretically wait until the end of the year.

But most of the unfinished business needs to be handled by Sept. 30, when government funding expires. Lawmakers are leaving Washington at the end of July and not returning until early September.

In short, Congress has a long way to go, and scant time to get there. Here are some key health policy issues for the remainder of 2025:

Physician reimbursements

Lawmakers have been searching for a way to reverse shrinking Medicare rates for several years. The original House version of the tax bill featured a pay increase for next year and would have tied future updates to the Medicare Economic Index. But the Senate scrapped those provisions in the final bill in favor of a one-year, 2.5% raise. The physician lobby seeks a more enduring fix.

Exchange subsidies

The enhanced premium tax credits created as COVID-19 relief and later extended will run out at year-end. The nonpartisan Congressional Budget Office estimates 5.1 million people will become uninsured if they are not renewed. Democrats, some Republicans, state officials and a broad swath of the healthcare sector are clamoring to keep them in place.

The Statutory Pay-As-You-Go Act of 2010 requires the executive branch to order spending cuts when new laws add to the deficit over five or 10 years, as Trump’s tax measure does. If Congress does not waive this rule — as it has in the past — Medicare cuts exceeding $500 billion over a decade would take effect starting next year. Preventing that would entail Republicans securing Democratic cooperation after shutting the minority party out of the tax debate.

Site-neutral payment

House Republicans may revisit legislation to bar hospitals from adding facility fees or other extra charges to bills for outpatient services under Medicare, Budget Committee Chair Jodey Arrington (R-Texas) told Bloomberg News.

Medicare Advantage rules

Congress has been trying for more than a year to codify Centers for Medicare and Medicaid Services regulations to speed up prior authorizations in Medicare Advantage, but has fallen short. Lawmakers have renewed the push, and likely will try to attach a measure to the fiscal 2026 federal funding package. More controversially, legislation that targets “upcoding” in the program were floated for the tax bill. Since such measures save tens of billions of dollars, they may resurface.

More Medicaid cuts

The House GOP may revive plans to reduce the enhanced Medicaid funding provided to expansion states under the Affordable Care Act of 2010, Arrington told Bloomberg News. That could end the expansions in up to nine states that have “trigger laws” on the books that halt expansions if federal support diminishes.

Medicare payment models

Bonus payments linked to advanced alternative payment models meant to spur value-based care in Medicare expired last year. Participants still get a 0.75% boost, but even that came close to disappearing under the House version of the tax bill. Supporters in Congress want at least some of the expired bonuses restored, but perhaps in a less generous form.

Expiring programs

Congress often extends healthcare programs for relatively short periods because it minimizes the near-term effects on the deficit.

This practice leaves providers in perpetual uncertainty over when, whether and for how much their particular programs or issues will be dealt with. Most of these expire Sept. 30.

They include:

• Telehealth authorities expanded during the pandemic that spurred mass adoption, particularly for mental healthcare and in rural areas. Lawmakers have repeatedly proposed two-year and permanent renewals that didn’t come to fruition. The policy is popular, but the length of an extension is up in the air.
• Medicare reimbursement flexibilities for hospital-at-home services also will sunset. A proposal that almost made it into the tax package would have extended the acute care hospital-at-home program for five years. That may come back.
• Safety-net hospitals face $8 billion in annual Medicaid disproportionate share hospital payment cuts unless Congress delays them, as it has before, or abolishes them altogether.
• Community health centers get both annual discretionary and multiyear mandatory funding, but both streams have been caught up in budgetary and partisan battles in recent years. Each must be renewed, and the long-term funding became more vital to federally qualified centers in light of the recently enacted Medicaid and exchange cuts. An increase also could be in the offing.
• The low-volume hospital payment adjustment for rural facilities and the Medicare-dependent hospital program for those with large numbers of older patients are expiring.
• The Medicare physician reimbursement work geographic practice cost index, designed to boost rural doctor pay, is due to sunset.
• The children’s hospital graduate medical education program provides funding for residents. Congress has provided multi-year funding in the past, but this policy has been mired in budget drama on Capitol Hill for several years.
• Funding for a Medicare quality measurement program is slated to run out.
• A Medicare initiative for type I diabetes research and a diabetes program for Native Americans both need renewal.
• “Conrad 30″ waivers that allow foreign medical school graduates to work in U.S. hospitals and ease staffing shortages must be reauthorized.
• Some programs relating to pandemic preparedness and the opioid crisis have been extended, but significant parts of those initiatives have expired.

NOTE FROM THE NATIONAL COUNCIL:

The FY26 appropriations process is underway. While we haven’t seen text of Labor-HHS funding bills yet, the President’s budget request from earlier this year proposed $94.7 billion in discretionary funding for the Department of Health and Human Services for FY26, which begins Oct.1. That would represent a massive decrease from the $127 billion budgeted in FY25.

Coupled with the recent cuts to Medicaid through reconciliation, these proposed cuts through the appropriations process would significantly worsen efforts to provide mental health and substance use treatment and care. We need to continue speaking out and letting elected officials know how important it is to preserve this funding!

Now is the time to take action to ensure lawmakers know that funding and critical mental health and substance use programs matter to you.

Use this link to send a note directly to your lawmakers with a pre-written message that you can edit urging them to secure federal funding for key programs across the continuum.