In his surprise announcement, 51-year-old Fitzgerald, Attorney for the Northern District of Illinois, said he would step down officially on June 30, and leave the Justice Department after serving nearly 24 years.
Fitzgerald was appointed by former President George W Bush and began serving in the post on September 1, 2001. He was kept on by President Barack Obama and ended up serving for nearly 12 years, making him the longest serving US attorney ever in Chicago.
Fitzgerald praised the career attorneys in the Northern District of Illinois, where he presides.
"I tried not to get in their way," he said.
Fitzgerald said he has no future employment plans and, after this summer off, the father of two young children will "consider his career options."
The announcement came as a bit of surprise to Justice Department officials who had been informed of his decision, CNN reported.
US Attorney General Eric Holder praised Fitzgerald for his commitment to serve "the American people and the citizens of Illinois with the utmost integrity and a steadfast commitment to the cause of justice."
"Over the years he has gained the trust of two Presidents and the unwavering confidence of four Attorneys General, and I am deeply grateful to him for his service and his friendship over the years," Holder said in a statement.
Fitzgerald was leading the prosecution of Headley and Tahawwur Rana in Chicago for participating in plotting the November 2008 terrorist attacks in Mumbai and planning to attack a Danish newspaper.
Fitzgerald first became widely known when he participated in the prosecution of Omar Abdel Rahman for the 1993 bombing of the World Trade Center. He also helped prosecute the terrorism defendants tied to the 1998 bombings of the US embassies in Kenya and Tanzania.
He also prosecuted the case of Blagojevich, the former Illinois governor who was convicted last year of corruption charges in connection with his efforts to profit from appointing the successor to the US Senate seat vacated by Barack Obama when he became president.
Speculation about Fitzgerald's future in legal circles has included the possibility of his being named FBI director to succeed Robert Mueller, whose term expires in September, though lucrative offers may be forthcoming from the private sector, the CNN reported.
