Trump and Haley confirmed reports of her resignation during a joint news conference at the White House Tuesday morning.
The president said that Haley had told him six months ago that she wanted to take some time off. Trump said Haley is welcome to rejoin his administration.
“You can have your pick,” Trump said, hinting she could be taking on a different role in the future.
“You’ve done a fantastic job and thank you very much,” the president added.
WATCH: Nikki Haley says serving as UN ambassador was ‘honour of a lifetime’
Haley also thanked Trump for the opportunity, saying it has been “an honour of a lifetime.”
She put to rest rumours that she will be running in the 2020 election, saying she plans on campaigning for Trump.
Haley said she will remain UN ambassador until the end of 2018 to ensure a smooth transition to the next ambassador. Trump said Haley’s successor will be announced in the next two or three weeks.
WATCH: Trump says Nikki Haley made UN ambassador a ‘more glamourous position’
The UN ambassador is a senior member of Trump’s administration. She was appointed to the post in November 2016.
Haley is the latest in a long list of senior staff members to leave the Trump administration, including former Secretary of State Rex Tillerson who was fired in March.
While Haley did not give a reason for her resignation, had been open about not always agreeing with the president.
WATCH: Nikki Haley praises Jared Kushner and and Ivanka Trump
Last month, she wrote an op-ed article 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.
“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.”
WATCH: U.S. Defence Secretary Mattis says Nikki Haley has been ‘wonderful representative’ for U.S.
— With files from Reuters, The Associated Press