Julia Pierson offered her resignation to the Secretary of the Department of Homeland Security on Wednesday.
Joseph Clancy, a former special agent in charge of the Presidential Protective Division of the agency, has been appointed to step in.
The move follows a major breach of the White House security on 19 September.
"Today Julia Pierson, the Director of the United States Secret Service, offered her resignation,
and I accepted it," Secretary of Homeland Security Jeh Johnson wrote in a statement.
"I salute her 30 years of distinguished service to the Secret Service and the Nation."
Obama also expressed his appreciation to Pierson for her long history of public service, White House spokesman Josh Earnest told
reporters on Wednesday.
Pierson offered her resignation because "she believed it was in the best interests of the agency to which she has dedicated her career", Earnest added.
High-ranking members of the US Congress had been calling for Pierson's resignation in the wake of her testimony before a House oversight committee on Tuesday.
There she acknowledged the Secret Service security plan was "not executed properly" during a recent breach of the White House.
On September 19, suspect Omar Gonzalez, 42, allegedly scaled a fence and gained entry to the famed US residence while carrying a knife.
On Wednesday, Gonzalez pleaded not guilty to charges against him, including entering a restricted building or grounds while carrying a
deadly or dangerous weapon.
Prosecutors say he jumped the main fence around the White House and gained entry inside through an unlocked door, then barrelled past a
guard and ran into the East Room before being tackled.