President Donald Trump named the executive secretary of the National Security Council, retired Lt. General Joseph Keith Kellogg, to serve as acting national security advisor until Flynn's successor is determined, the White House said in a statement.
Flynn's departure came less than a month after he took office.
He has been under fire following revelations that he discussed with Russia's ambassador the sanctions that the previous administration of President Barack Obama imposed on Moscow in December before he officially assumed office as national security advisor.
His trouble deepened as he was found late last week to have lied to Vice President Mike Pence about his contact with the Russian envoy.
"I inadvertently briefed the Vice President Elect and others with incomplete information regarding my phone calls with the Russian Ambassador. I have sincerely apologized to the President and the Vice President, and they have accepted my apology," Flynn said in his resignation letter.
Flynn's resignation came just days after North Korea test-fired a newly developed intermediate-range ballistic missile in the first provocative act since Trump took office. Trump said earlier Monday that the North is a "big, big problem" and he will deal with it "very strongly."
Flynn has also been a strong advocate of the U.S. alliance with South Korea.