His abrupt departure was announced an hour after Trump told reporters he was disappointed in Price's use of private aircraft and did not like the optics of it.
"Secretary of Health and Human Services Thomas Price offered his resignation earlier today and the president accepted," the White House said in a statement.
Trump named Don Wright to serve as acting secretary. Wright is currently the deputy assistant secretary for health and director of the office of disease prevention and health promotion.
"I'm not happy. OK? I'm not happy," Trump told reporters on the White House South Lawn.
Candidates to succeed Price included Seema Verma, who is administrator of the Centers for Medicare and Medicaid Services and who is close to Vice President Mike Pence, and Scott Gottlieb, a physician who serves as commissioner of the Food and Drug Administration.
The resignation leaves Trump with a second Cabinet position to fill. He has yet to pick a secretary for homeland security after hiring former Secretary John Kelly as his White House chief of staff.
It was the latest blow to the Trump White House, which has struggled to get major legislative achievements passed by Congress and has been embroiled in one controversy after another since Trump took office in January.
Price, a former congressman, was instrumental in the Trump administration's policies aimed at undercutting Obamacare, as well as working with governors across the country to slowly begin unravelling parts of the law.
In a resignation letter, Price offered little in the way of contrition. He said he had been working to reform the U.S. healthcare system and reduce regulatory burdens, among other goals.
"I have spent forty years both as a doctor and public servant putting people first. I regret that the recent events have created a distraction from these important objectives," he said.
Trump, currently trying to sell his tax cut plan and oversee the federal response to devastation wreaked by three hurricanes, saw the Price drama as an unnecessary distraction and behind the scenes was telling aides "what was he thinking?," a source close to the president told Reuters.
Price promised on Thursday to repay the nearly $52,000 cost of his seats on private charter flights. "The taxpayers won't pay a dime for my seat on those planes," Price said.
But that was not enough to satisfy Trump.
Trump told reporters that the "optics" of Price's travel were not good since, as president, he is spending a lot of time trying to renegotiate U.S. contracts to get a better deal for taxpayers.
"Look, I think he's a very fine person. I certainly don't like the optics," Trump said.
Price had also been seen in the White House as having been ineffective in getting Congress to pass healthcare reform legislation, an effort that has fizzled on Capitol Hill.
Price was one of a handful of senior officials in Trump's administration put on the defensive over reports about their use of charter flights and government aircraft, sometimes for personal travel, when they could have flown commercial for less money.
Presidential aides said Trump was considering imposing a ban on use of private charter planes by Cabinet officials.
The Washington Post on Friday reported that Veterans Affairs Secretary David Shulkin attended a Wimbledon tennis match, toured Westminster Abbey and took a cruise on the Thames this summer during a 10-day trip to discuss veterans' health issues in Britain and Denmark.
Shulkin, who travelled on a commercial airline, was accompanied on the trip by his wife, whose airfare was paid for by the government and who received a per diem for meals, the Post said, noting that the Department of Veterans Affairs said she was travelling on "approved invitational orders."
His six-person travelling party included an acting undersecretary of health and her husband as well as two aides. They were accompanied by a security detail of as many as six people, the Post said.
Washington news media outlet Politico has reported that Price had taken at least two dozen private charter flights since May at a cost to U.S. taxpayers of more than $400,000.
Senior U.S. government officials travel frequently, but are generally expected to keep costs down by taking commercial flights or the train when possible.
Environmental Protection Agency Administrator Scott Pruitt and Treasury Secretary Steve Mnuchin have also been in the spotlight for their travel habits.
(This story has not been edited by NDTV staff and is auto-generated from a syndicated feed.)