Officials said they would quickly appeal.
The judge also stayed Health Secretary Robert F. Kennedy Jr.’s appointments to the CDC’s vaccine advisory committee.
Stay of Vaccine Schedule Update
The CDC, with backing from Kennedy, in January stopped broadly recommending six vaccines for children, including shots against rotavirus, hepatitis A, and influenza. The move did not involve the Advisory Committee on Immunization Practices (ACIP).
Officials took the step in response to an executive order from President Donald Trump that directed them to review vaccine recommendations in peer countries and, if appropriate, revise the U.S. recommendations.
Department of Health and Human Services officials said that just one of 20 countries they studied recommended hepatitis A vaccination for children. They also found that most countries did not recommend influenza vaccination for children, and a handful did not recommend the rotavirus vaccine for kids.
Murphy determined that the update was arbitrary and capricious because it “abandoned the agency’s longstanding practice of getting recommendations from ACIP before changing the immunization schedules without sufficient explanation.”
ACIP Appointments Blocked
Murphy also sided with the American Public Health Association and other plaintiffs against Kennedy’s remaking of ACIP, which provides advice to the CDC on immunization practices.
Kennedy removed all ACIP members in 2025, citing conflicts of interest, and has, over several rounds, named new members to the panel.
Plaintiffs said the appointments violated the Federal Advisory Committee Act in part because the remade committee is unfairly balanced, as some new members do not have experience in vaccine-related fields.
Murphy said he acknowledged that many of the individuals Kennedy selected have extensive expertise, but not all of them have expertise related to vaccines.
“ACIP is not just a committee of doctors, or even a committee of public health experts; it is a committee specifically dedicated to the ‘use of vaccines and related agents for effective control of vaccine-preventable diseases,’” Murphy said. “As to that specific function, the newly appointed members appear distinctly unqualified.”
Dr. Robert Malone, one of the new members, who helped invent the technology used in some COVID-19 vaccines, wrote on his blog that the court was “substituting its own definition of relevant expertise for the Secretary’s.” He said the panel considers a number of aspects, such as public health policy, in which members criticized by the judge have valuable expertise.
Murphy stayed Kennedy’s appointments, prompting the CDC to cancel an ACIP meeting that had been scheduled to begin on Wednesday.
Because the appointments were illegally carried out, votes by the remade ACIP must also be blocked, the judge decided.
Officials Except Decision to be Overturned
Murphy has issued a number of decisions against the Trump administration, including an injunction preventing the government from deporting illegal immigrants to countries other than their home country, which have been overturned by higher courts.
Officials said that they expect the same with the latest ruling.
“How many times can Judge Murphy get reversed in one year? The same day he is stayed for repeatedly refusing to follow the law, he issues another activist decision,” Todd Blanche, the deputy attorney general, wrote in a post on X. “We will keep appealing these lawless decisions, and we will keep winning.”
Andrew Nixon, a spokesman for the Department of Health and Human Services, said in a post on X that the administration looks forward to the judge’s decision being overturned.
“We are thrilled that the court has discarded the baseless vaccine schedule changes made by Secretary Kennedy and is blocking the Advisory Committee on Immunization Practices from doing further damage to vaccine policy,” Richard Hughes IV, an attorney representing the organizations and a former Moderna executive, said in a statement.
Dr. Georges Benjamin, CEO of the American Public Health Association and a former consultant to GlaxoSmithKline, added that the injunction “underscores the need for using science in public health decision-making and using a process that engages qualified experts when it comes to recommending interventions that impact human health.”
