The retirement of Thomas, the longest-serving White House reporter, was announced by Hearst Corp., where she worked as a newspaper columnist after spending most of her career with United Press International (UPI).
"Helen Thomas announced Monday that she is retiring, effective immediately," Hearst News Service said.
Thomas had spent the weekend in the eye of a political firestorm, over remarks she made about Israel during a May 27 "Jewish Heritage Celebration" at the White House, which surfaced last week in a YouTube video.
Asked at the event by the website RabbiLive.com whether she had any "comments on Israel," Thomas replied: "Tell them to get the hell out of Palestine.
"Remember these people are occupied and it's their land, not German and not Poland," Thomas said. "They can go home, Poland, Germany, and America and everywhere else."
White House spokesman Robert Gibbs on Monday described the remarks as "offensive and reprehensible" and Thomas issued an apology on her website, HelenThomas.org.
"I deeply regret my comments I made last week regarding the Israelis and the Palestinians," she said.
"They do not reflect my heartfelt belief that peace will come to the Middle East only when all parties recognize the need for mutual respect and tolerance. May that day come soon," Thomas said.
The White House Correspondent's Association (WHCA) board said Monday that Thomas's comments were "indefensible."
"Many in our profession who have known Helen for years were saddened by the comments, which were especially unfortunate in light of her role as a trailblazer on the White House beat," the board said.
The board noted Thomas was not currently a member of the association and said "the incident does revive the issue of whether it is appropriate for an opinion columnist to have a front row seat in the briefing room."
Thomas had been scheduled to deliver a June 14 graduation address at Walt Whitman High School in Bethesda, Maryland, outside Washington, but the school said Sunday it had cancelled her appearance.
"Graduation celebrations are not the venue for divisiveness," Whitman principal Alan Goodwin said in an email to parents at the school.
"Graduation is the time for a cohesive and joyous celebration of our students' achievements; other forums exist for discussions of political issues," Goodwin said.
Thomas posed what now seems likely to be her final question to a US president -- Obama, during a news conference in the East Room at the White House on May 27.
"Mr President, when are you going to get out of Afghanistan? Why are we continuing to kill and die there? What is the real excuse? And don't give us this Bushism, 'if we don't go there, they'll all come here.'"
Thomas, who won multiple journalism awards and was awarded a string of honorary degrees, arrived at the White House in 1960, after covering Kennedy's campaign and traveled the world following subsequent presidents.
Her latest book "Listen Up Mr President" was published in 2009.