The order advances a long-standing goal of Health Secretary Robert F. Kennedy Jr., an anti-vaccine activist who has promoted a link between vaccines and autism that scientists have repeatedly debunked.
Public health experts say the US schedule reflects decades of evidence and the specific health needs of Americans, and that fewer recommended shots will leave more children exposed to preventable diseases.
The order also recommended splitting the childhood measles, mumps and rubella vaccine into three shots and delivering the shots at separate medical visits.
Kennedy had in January cut the US immunisation schedule to remove shots against six out of 17 diseases, a move halted by a federal court ruling. The Trump order says the federal government will now only support the remaining 11 shots.
The American Academy of Pediatrics and vaccine maker Merck criticised the order.
"We are evaluating our next steps," said Richard Hughes IV, lead counsel for the American Academy of Pediatrics, which sued earlier this year over Kennedy's changes to the childhood immunisation schedule.
Merck said there is no published scientific evidence showing any benefit to splitting the combination MMR shot into three, and that using the individual components increases the number of injections and can lead to delayed or missed immunisations.
"Effective immediately, my administration is recognising gold-standard childhood vaccine recommendations for only 11 core vaccinations against the most serious and dangerous diseases, along with the MMR, which hopefully will be split up," Trump said during a White House signing ceremony.
Demetre Daskalakis, former director of the CDC's National Centre for Immunisation and Respiratory Diseases, said breaking up combination vaccines and downgrading recommendations would deepen disparities and worsen vaccine coverage.
Kennedy has previously led efforts to drop universal recommendations for hepatitis B shots for children and reduce the list of recommended vaccines, citing links to autism that scientists have repeatedly debunked.
The executive order says it reaffirms Kennedy's overhaul despite the ongoing litigation.
Republican Senator Bill Cassidy of Louisiana, a physician who chairs the Senate health committee, condemned the order.
"I'm a doctor. This executive order is wrong. The president does not have the expertise to make these changes," Cassidy said, adding that breaking up vaccines "will mean children have to get more shots to get the same protection, not fewer shots."
Cassidy, however, has shepherded Trump's slate of health agency leaders through confirmation despite his own warnings about vaccine scepticism. He cast a decisive vote to confirm Kennedy in 2025. Cassidy lost his Republican primary in May to a Trump-endorsed challenger and will leave office in January.
Trump, Kennedy and other White House officials said the order means US children would receive far fewer than the 72 injections recommended under the previous schedule.
Vaccine experts say that figure is inflated, because it counts combination shots such as MMR as multiple injections even though they are given in one shot, and assumes annual flu and COVID-19 doses.
with AP
9°C