Homeland Security Director Jeh Johnson announced the resignation in a statement. He also announced that the Department of Homeland Security would take over an internal inquiry of the Secret Service and that he would appoint of a new panel to review security at the White House.
Joseph Clancy, formerly a special agent in charge of the Presidential Protective Division of the Secret Service, was named interim director, Johnson said in his statement.
Calls for Pierson to leave her post grew after a poor performance during her testimony Tuesday on Capitol Hill and another bombshell revelation the same day that an armed security contractor was allowed to get into an elevator with the President
during a recent trip to the Centers for Disease Control in Atlanta.
Even some high-ranking Democrats had turned against Pierson, who was in the job for less than two years. In an interview on Wednesday, Rep. Elijah Cummings, the top Democrat on the House Oversight Committee, where Tuesday's hearing took place, said he thought Pierson -- who he referred to as "this lady" -- "has to go."
The Maryland congressman reiterated this stance in an interview with CNN's Wolf Blitzer. "I want her to go if she cannot restore trust in the agency and if she cannot get the culture back in order," he said.
And New York's Chuck Schumer, the third-ranking Democrat in the Senate, had announced he would call for Pierson's resignation on Wednesday as well, though that was later canceled.
Republicans also had called for Pierson to step down.
"It's clear to me that the only way to solve the problem the Secret Service has is with new leadership," Sen. Lindsey Graham of South Carolina said. "What Julia Pierson describes as mistakes are major security failures on multiple fronts."
Graham said light security around Obama is "the worst possible signal to send to terrorists and our enemies around the world."
After news of her resignation broke, lawmakers praised her decision to step down.
"The agency tasked with protecting the highest office in our land should be the crown jewel of federal law enforcement," Rep. Jason Chaffetz, who sits on the Oversight Committee, said in a statement Wednesday afternoon. "I will work with my colleagues and the Administration towards returning the agency back to the standards the President deserves."
News of Pierson's resignation came as new information about the fence-jumper came to light.
Omar Gonzalez, 42, pleaded not guilty to federal and District of Columbia charges
on Wednesday. A federal judge in Washington ordered additional mental testing on the 42-year-old Iraq war veteran to determine whether he is competent to stand trial.
Meanwhile, the inquiry continues into how the Army veteran launched over the fence and was able to sprint up to the front door, burst into the White House and run into the ornate East Room.
Neither President Barack Obama nor the first family were at home at the time of the incident.
But a Secret Service source told CNN there is an elaborate closed-circuit video system, and that video is being dissected to establish new protocols.
When Gonzalez burst through the White House door, he pushed a female officer to the side.
But the source said, "Gender was not a factor, she got one door secured but was pushed over while trying to get second door shut."
An alarm box had been turned down near the front door after complaints by the White House usher's office that it was too loud.
A canine unit was not released to chase Gonzalez, said the source, because there were "too many friendlies around."
Pierson was named the director of the U.S. Secret Service in March 2013, tapped by Obama to change the culture of an agency that was then marred by a Colombian prostitution scandal.
Several male agents in an advance contingent before a presidential trip to Cartagena, Colombia, had taken prostitutes back to their hotel rooms, according to investigations after the trip. A morning-after dispute between one agent and a woman over payment led to exposure of what happened and the ensuing investigations. Nine agents eventually left or lost their jobs
Pierson became the Secret Service's chief of staff in 2008. Before that, she served on the protective details of Presidents George H.W. Bush, Bill Clinton and George W. Bush. She had been the assistant director of the agency's Office of Human Resources and Training, and held the title of deputy assistant director in the Office of Protective Operations and the Office of Administration.
Pierson started her career in law enforcement as a police officer in Orlando, Florida. She joined the Secret Service in 1983, working in the Miami and Orlando field offices.
Johnson made sure to praise the overall work of the Secret Service when he announced Pierson's resignation.
"It is worth repeating that the Secret Service is one of the finest official protection services in the world, consisting of men and women who are highly trained and skilled professionals prepared to put their own lives on the line in a second's notice for the people they protect."