The 77-year-old veteran diplomat entered the plea in federal district court in Maryland as part of a deal in which prosecutors would recommend he serve no more than five years in prison.
Asked by judge Theodore Chuang if he was guilty, Bolton replied: “I am, your honour, and I’m sorry for it.”
He will also have to pay a fine of US$2.25 million.
Bolton, one of several Trump foes to be hit with criminal charges since the Republican president returned to the White House, was indicted in October on 18 counts of transmitting and retaining top secret national defence information.
He was accused of sharing classified files by email with two “unauthorised individuals” who have not been identified but are believed to be his wife and daughter.
The material was allegedly later used in a book that Bolton wrote, “The Room Where It Happened,” that was highly critical of the Trump administration.
Bolton, who served as Trump’s national security advisor during his first term, frequently appears on television news shows and in print to condemn the man he has called “unfit to be president.”
Trump has repeatedly lashed out at his former aide and withdrew his security detail shortly after returning to the White House in January of last year.
The Trump Justice Department has sought to bring cases against other prominent critics of the president, including New York Attorney General Letitia James and former FBI director James Comey.
Sentencing has been scheduled for October 28.
