Donald Trump has said UN ambassador Nikki Haley will leave his administration “at the end of the year”.
The president spoke as he and Ms Haley met in the Oval Office, shortly after word came of her plans to resign.
He called her a “very special” person, adding that she told him six months ago that she might want to take some time off. Mr Trump said that together they had “solved a lot of problems”.
It is the latest shake-up in the turbulent Trump administration, weeks before the November midterm elections.
No reason for the resignation was immediately provided.
Ms Haley, 46, was appointed to the UN post in November 2016 and last month co-ordinated Mr Trump’s second trip to the United Nations, including his first time chairing the Security Council.
Before she was named by Mr Trump to her UN post, she was governor of South Carolina, the first woman to hold the post. She was re-elected in 2014.
Last month she wrote an article in the Washington Post discussing her policy disagreements but also her pride in working for Mr Trump.
It came in response to an anonymous essay in the New York Times by a senior administration official that alleged there was a secret “resistance” effort from the right in the administration and internal discussions of invoking the 25th amendment to remove Mr Trump from office.
“I proudly serve in this administration, and I enthusiastically support most of its decisions and the direction it is taking the country,” Ms Haley wrote. “But I don’t agree with the president on everything.”
As South Carolina governor, she developed a national reputation as a racial conciliator who led the charge to bring down the Confederate flag at the Statehouse and guided the state through one of its darkest moments, the massacre at a black church.