Trump spoke as he and Haley met in the Oval Office, shortly after word came of her plans to resign.
He called Haley a "very special" person, adding that she told him six months ago that she might want to take some time off. Trump said that together, they had "solved a lot of problems."
It's the latest shake-up in the turbulent Trump administration just weeks before the November midterm election.
No reason for the resignation was immediately provided.
Haley, 46, was appointed to the U.N. post in November 2016 and last month coordinated Trump's second trip to the United Nations, including his first time chairing the U.N. Security Council.
Before she was named by Trump to her U.N. post, Haley was governor of South Carolina, the first woman to hold the post. She was re-elected in 2014.
Last month Haley wrote an op-ed in The Washington Post discussing her policy disagreements but also her pride in working for Trump. It came in response to an anonymous essay in The New York Times by a senior administration official that alleged there to be a secret "resistance" effort from the right in Trump's administration and that there were internal discussions of invoking the 25th amendment to remove 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," Haley wrote. "But I don't agree with the president on everything."
As 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 South Carolina through one of its darkest moments, the massacre at a black church.
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