She will be the third senior official working on national security issues to resign since Sunday.
South Korea's national security adviser was in Washington on Wednesday for his first meeting with his new American counterpart, John Bolton, U.S. officials said, amid preparations for separate U.S. and South Korean summits with North Korea.
Schadlow was promoted to deputy national security adviser for strategy in January following the departure of Dina Powell, a former NSC official and Goldman Sachs executive, and was a key author of the president's National Security Strategy document, which laid out Trump's national security goals and approach. "President Trump thanks him for his patriotic service and wishes him well".
She was tapped in January to take over for Dina Powell, who chose to step down previous year as Deputy National Security Adviser.
Bossert, who was a former deputy national security adviser to former President George W. Bush, had overseen the Trump administration's response to the Hurricane Maria disaster in Puerto Rico, as well as cybersecurity policy.
"Together, we captured your vision for a strong and confident American and developed your America First National Security Strategy - which turned that vision into a strategic direction for your administration", Schadlow wrote.
"Tom is a very smart and highly skilled national security leader who has been a beacon of principle, capability, and discipline in an otherwise chaotic White House", he said in a statement.
News of her resignation comes a day after the White House's homeland security adviser Tom Bossert was unexpectedly pushed out on Tuesday, a move driven by Bolton's desire to put his own team in place.
The National Security Council is expected to see more changes in the coming weeks under Bolton's leadership, according to reports. The NSC's human resources department has reportedly asked high-level staffers to submit their resumes if they're not already in the system.