Trump said Kevin McAleenan, the current commissioner of U.S. Customs and Border Protection, would serve as acting secretary.
This is a developing story. According to the New York Times, Trump had a habit of calling Nielsen "at home early in the mornings" to demand she refuse to accept asylum petitions from Central Americans (which she could not lawfully do).
Trump announced the resignation in a tweet today.
Replacing her on an acting basis will be Kevin McAleenan, who now serves as the commissioner of Customs and Border Protection, Trump said Sunday.
The meeting was taking place amid an ongoing influx of migrants at the U.S. -Mexico border that has been taxing America's immigration system and sparking frustration within the White House. She is now a 2018-2019 Reveal Fellow at the Center for Investigative Reporting.
President Donald Trump has spent the last several months pushing his administration to crack down on migrant families, despite issuing an executive order in June ending the family separation policy. The sources say she has been frustrated by difficulty getting other departments to help with the growing number of families coming crossing the border.
Nielsen's departure was first reported by CBS News. The announcement of her departure came shortly after the meeting.
Nielsen advocated for strong cybersecurity defense and often said she believed the next major terror attack would occur online - not by planes or bombs. Minority Leader Chuck Schumer, "you know he's completely lost touch with the American people".
He and Kirstjen Nielsen parted ways after urgent talks in the White House that followed a two-day visit to California, during which they viewed parts of the renovated border wall.
The dissonance between Mr. Trump and Ms. Nielsen was particularly pronounced of late as the Secretary struggled to keep up with her boss's agenda.
Ultimately, acting White House chief of staff Mick Mulvaney seemed to have been able to talk the President out of closing the port of El Paso.
"We need steady, informed and effective leadership in the administration and in Congress to have any hope of fixing our out-of-control border security and immigration problems", Johnson said Sunday evening.