Fitzgerald, 51, is the longest-serving United States Attorney for the Northern District of Illinois, having served since his appointment Sept. 1, 2001. The resignation is effective June 30.
He was formerly an assistant U.S. attorney in New York and is leaving the Justice Department after nearly 24 years.
"When I was selected for this position in 2011, I said that it was one of the greatest opportunities that one could ever hope for, and I believe that even more now after having the privilege of working alongside hundreds of dedicated prosecutors and agents," he said in a statement.
As U.S. attorney in Chicago, Fitzgerald prosecuted hundreds of high-profile cases from rigged city hiring, organized crime and corporate fraud to drug trafficking and foreign terrorism. His office successfully prosecuted two former Illinois governors, Republican George Ryan and Democrat Rod Blagojevich, for public corruption and both are serving sentences in federal prisons.
"A hallmark of Pat's tenure has been his personal commitment to the department's mission and his willingness to accept the call of duty -- whenever it came and whatever it required," said U.S. Attorney General Eric Holder. "In 2003, he was appointed as special counsel in the investigation into the disclosure of the identity of a covert employee of the Central Intelligence Agency that resulted in the indictment of I. Lewis "Scooter" Libby, then chief of staff and national security adviser to ... Vice President [Dick Cheney]."
Libby was convicted of perjury and obstruction of justice.