Nielsen resigned, two people familiar with the matter told the Associated Press. She went into a meeting with Trump at the White House in Sunday not knowing whether she'd be fired or would resign, and she ended up resigning, they said.
Sources said she has been frustrated by difficulty getting other departments to help with the growing number of families coming crossing the border.
Trump thanked Nielsen for her service and named Kevin McAleenan as the acting homeland security secretary.
"I have confidence that Kevin will do a great job!" Trump said. McAleenan is a longtime border official who is well-respected by members of Congress and within the administration. The decision to name an immigration officer to the post reflects Trump's priority for a sprawling department founded to combat terrorism following the Sept. 11 attacks.
Nielsen had been on the chopping block before. Trump threatened to fire her and she previously considered resigning, but officials at the time recognized there were no obvious successors in place.
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Trump nominated Nielsen to lead the Department of Homeland Security in October 2017, and she was sworn in weeks later. She previously served at the Department of Homeland Security as the chief of staff for John Kelly before he left to become the White House chief of staff. She followed him to the White House, where she worked as an assistant to the president and the principal deputy chief of staff.
Before Nielsen's work for the current administration, she consulted on homeland security and preparedness matters, according to her biography on the website for George Washington University's Center for Cyber and Homeland Security, where she was a senior fellow.
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SEE ALSO: List of notable Trump administration resignations, firings and departures
The Associated Press contributed to this report.