Pierson, who had been in her position since March 2013, faced growing calls from lawmakers to step down in the fallout from a Sept. 19 incident in which an Iraq war veteran with a knife clambered over the White House fence, sprinted across the lawn and got deep inside the mansion before an off-duty agent stopped him.
Pierson had told a congressional committee on Tuesday she took "full responsibility" for security lapses. On Wednesday, she offered her resignation in a meeting with Homeland Security Secretary Jeh Johnson, who accepted it.
Pierson's resignation came a day after the disclosure that in a violation of protocol, an armed private security contractor with a criminal record rode on an elevator with Obama in Atlanta earlier this month and took pictures and video of the president on his phone.
The lapses, along with a 2011 incident in which seven gunshots were fired at the White House, had raised concerns across Washington that Obama is as not as protected as he should be in an age of global tumult.
While all presidents have faced death threats, Obama, as the first African-American president, is believed to have received more than his predecessors.
When she was appointed the first female director of the Secret Service, Pierson was given the mission of cleaning up the agency's culture after a 2012 presidential trip to Colombia in which up to a dozen agents were found to have hired prostitutes.
An episode last March did not help her reputation. Three agents responsible for protecting Obama in Amsterdam were sent home and put on administration leave after what was described as a night of drinking.
White House spokesman Josh Earnest said Obama believed Pierson's resignation was in the best interest of the agency, and that "recent and accumulating" reports of security lapses led the president to conclude new leadership was required at the Secret Service.
Calls for Pierson to step down had grown on Capitol Hill prior to her resignation. The 30-year Secret Service veteran had failed to inspire confidence among lawmakers from both parties during a 3-1/2-hour grilling on Tuesday before the House Oversight and Government Reform Committee.
Representative Darrell Issa, who led a grilling of Pierson in the House Oversight and Government Reform Committee on Tuesday, said he was doubtful one resignation would produce the kind of change needed.
"Problems at the Secret Service pre-date Ms. Pierson's tenure as director, and her resignation certainly does not resolve them," he said.
In response to calls from lawmakers for an independent probe into the Sept. 19 fence-jumping incident, the Homeland Security Department will establish a panel of independent experts to investigate what happened.
Earnest said the group will recommend changes to how the Secret Service operates and suggest who might become the next permanent Secret Service director. A veteran of the agency's presidential protection division, Joseph Clancy, was named acting director in the meantime.
The Secret Service has already taken some steps to bolster security. It has established a barricade several feet away from the White House fence to deter further fence-jumping, and is contemplating a host of options for further measures.
But it faces a difficult balancing act, providing the necessary security while still allowing access to close-up views of the iconic white mansion, a symbol of democracy around the world.
Republican Representative Jason Chaffetz, who chairs a national security oversight subcommittee, questioned Pierson during the hearing on the number of times she had briefed Obama on incidents this year where his safety had been compromised.
She replied that there was only one such briefing - after the fence jumper incident. She made no mention of the Atlanta incident.
The omission prompted Chaffetz to call for her ouster, and he was later followed by others, including Democratic Senator Charles Schumer and Representative Elijah Cummings, the top Democrat on the Oversight Committee.
"Director Pierson's resignation is a matter of national security and I am pleased she is stepping down. The position should be filled immediately by new leadership from outside the Secret Service for a fresh start," Chaffetz said in a statement.
