Ongoing AAP, HHS Legal Battle Will Determine Future Health Care Action

The ongoing legal battle in American Academy of Pediatrics (AAP) et al. v. Kennedy et al. is considered a shakeup of the health care system, as a federal court recently intervened to halt sweeping changes to the national childhood immunization schedule.

Although the litigation is led by medical societies, the outcome carries heavy implications for the pharmacy profession, which now administers a substantial share of vaccinations across the United States.

“There is a lot of confusion, which is why it is important for pharmacists and pharmacy technicians to make sure that they are staying up to date with the ever-changing information so that current information is being provided to patients and their families,” Gretchen Garofoli, PharmD, BCACP, clinical professor in the School of Pharmacy at West Virginia University, told Drug Topics^®. “It is recommended to know your state’s scope of practice as far as which recommendations need to be followed for administration of vaccines by pharmacists, student pharmacists, and pharmacy technicians.”

She added that some states might require pharmacists, student pharmacists, and pharmacy technicians to administer vaccines based on the Advisory Committee on Immunization Practices (ACIP) recommendations, but other states follow recommendations from medical organizations such as AAP and the American Academy of Family Physicians.

A Sudden Shift in Federal Policy

The conflict reached a high point in March 2026, when US District Judge Brian Murphy issued a preliminary injunction that effectively froze the administration’s attempts to radically alter vaccine policy.¹

Spreeha Choudhury, PharmD, JD, associate at Epstein Becker Green and part of the AAP client team in the legal case, detailed the 2 core arguments that the plaintiffs, AAP et al, brought to the lawsuit. The plaintiffs argued that Kennedy and ACIP violated the Administrative Procedure Act (APA). They challenged the January 5, 2026, changes to the childhood immunization schedule, which decreased the number of recommended vaccines from 17 to 11 and moved others to shared clinical decision-making without ACIP involvement. They challenged the removal of the routine recommendation for the hepatitis B birth dose and the change to shared clinical decision-making, the removal of COVID-19 to shared clinical decision-making for all populations as well as removing the recommendation for pregnant women and children, and the removal of thimerosal from all influenza vaccines.

“The APA is the backbone of this case. The plaintiffs argue that HHS violated the APA because it bypassed the longstanding, evidence-based scientific review process for vaccine recommendations,” Choudhury said. “The district court agreed in a stay order issued in March 2026, finding the schedule changes were reviewable final agency actions because they directly affect provider liability, insurance coverage, and pharmacist authority to administer vaccines.”

The APA is a federal statute that governs how executive branch agencies, such as HHS and the CDC, create and change different policies, Choudhury said. Government officials are required to explain the changes with reasoned and documented justification.

“Agencies cannot simply discard the expert processes that normally inform them,” Choudhury said. “The APA also requires agencies to follow proper procedure. When Congress has built a specific process into a statute, such as ACIP's role in vaccine recommendations, agencies cannot bypass it.”

The APA also allows courts to review the final actions of the agency, and if an agency action fails the APA review, courts can stay or set the action aside.

In the second argument, the plaintiffs argued that the firing and reconstitution of ACIP violated the Federal Advisory Committee Act, which states that advisory groups should be fair and balanced. Choudhury added that the plaintiffs believe ACIP was not properly constituted by Kennedy, and so all votes taken by the committee after June 2025 are void.

Judge Murphy also stayed the appointments of 13 members to the ACIP and invalidated all votes taken by the committee since its reconstitution by HHS Secretary Robert F. Kennedy Jr. in June 2025.²

“Pharmacists were not named plaintiffs in the case,” Choudhury said. “However, given the volume of vaccines pharmacists administer nationwide, the outcome will significantly impact pharmacy practice.”

What Happens Next in the Legal Process

The case is still active in 2 parallel tracks, Choudhury said.

“At the District Court, plaintiffs are pursuing the administrative record, the documents the government relied on to support the challenged changes, and the reasoning behind them,” she said. “This discovery phase is critical because APA cases can be won or lost depending on the administrative record.”

Simultaneously, the March 2026 stay order is also on appeal by the First Circuit Court of Appeals, with a major decision expected later in 2026. If the court rejects the administration’s appeal, the case could potentially reach the Supreme Court’s emergency docket or be argued in the next Supreme Court term beginning October 2025, according to Choudhury.

For major milestones, Choudhury said it would be important to see how the March 2026 stay order is implemented, specifically how Kennedy handles the new appointments to ACIP. Further, there have been no updated ACIP charters, which governs the committee’s composition, mission, and procedures. Choudhury added that the absence creates uncertainty about how the committee will proceed. It is important to know there was a draft charter published last month and then was rescinded.

Choudhury said that Kennedy could also continue making unilateral changes to vaccine recommendations in violation of the stay order, which would continue to bypass ACIP.

How Will This Impact Pharmacies?

The operational impact on pharmacies extends beyond liability to the very mechanics of patient care and billing. Because many insurance benefits are legally tied to ACIP recommendations, the administration's decision to bypass the formal committee process threatened the stability of vaccine coverage.

Amidst the instability, many pharmacists are looking toward professional medical organizations for clinical guidance. In several states, new regulations have been passed to establish the guidelines of the AAP, the American Academy of Family Physicians (AAFP), and the American College of Obstetricians and Gynecologists (ACOG) as the basis for vaccination authority when federal recommendations falter. Garofoli stated that some of her pediatrician colleagues have had parents with more questions and hesitancy as well as refusing vaccines for their children that they had not previously refused.

“This is where it comes back to pharmacists, student pharmacists, and pharmacy technicians ensuring that they are operating within their scope of practice in the state in which they work,” Garofoli said. “Working under their scope of practice covers the liability piece. All of the guidance says that insurances should continue to cover vaccines.”

She added that many insurance benefits are also tied to ACIP recommendations, which has added to the problematic nature of this action.

“Messaging that has been clear from multiple trusted health organizations is that the science has not changed regarding the recommendations, and mentioned in the injunction is one of the reasons for the lawsuit was that the changes made to the pediatric vaccine schedule were ‘arbitrary,’” Garofoli said. “Pharmacists need to continue to educate patients and their families on the importance of vaccinations and must be ready to answer any questions that they may have.”

Choudhury added that the case has implications for the legal foundation of pharmacy-based immunizations.

“When a vaccine shifts from ‘routine’ to [shared clinical decision making], that legal foundation becomes uncertain, raising questions about a pharmacist's authority under state law and the liability concerns that follow,” Choudhury said. “The [shared clinical decision making] designation, without additional CDC guidance on how to conduct [shared clinical decision making], has also created general confusion among providers about who to vaccinate.”

Conclusion

As the case moves forward, the final resolution of this case could eventually reach the Supreme Court, where it may define the limits of executive power over scientific policy for decades to come. For now, pharmacists are advised to stay closely informed of their specific state’s scope of practice and to continue educating families on the vital importance of maintaining the traditional immunization schedule.

Choudhury added that the case also represents increased judicial scrutiny of agency action. In the future, it could mean that courts will examine the decisions of federal health agency decisions when the procedures are bypassed.

“Going beyond vaccines, this case stands for accountability in public health and scientific policymaking and will be central to understanding the scope of executive power over scientific policy,” Choudhury said. “A ruling by the Supreme Court in favor of the government would establish that a single cabinet secretary can override decades of established science and process. A ruling for the plaintiffs would entrench the requirement that changes to scientific policy must follow the correct process, regardless of politics.”

References

1. Choi J. Federal court blocks Kennedy’s vaccine changes, invalidates vaccine advisory panel. The Hill. March 16, 2026. Accessed June 4, 2026. https://thehill.com/policy/healthcare/5786565-judge-blocks-kennedy-vaccine-changes/

2. Nowosielski B. Vaccine policy shifts erode patient and parent trust. Drug Topics. March 25, 2026. Accessed June 4, 2026. https://www.drugtopics.com/view/vaccine-policy-shifts-erode-patient-and-parent-trust