Flaggs said he also will leave his job as administrator of Warren County Youth Detention Center. He says he is considering a run for mayor of Vicksburg. The city's primary elections are set for May, and the general election will be in June.
He said he will make an announcement Jan. 12 on whether he will seek the City Hall spot. His retirement from the Legislature will be effective July 1.
"I'm going from two jobs to one job or no jobs," Flaggs said. "There's something to be said for leaving on your own time, your own terms."
The 59-year-old Flaggs is chairman of the House Corrections Committee. He previously served as chairman of the Juvenile Justice Committee and the Banking Committee.
Flaggs' current legislative term ends in 2014. By state law, Gov. Phil Bryant must set a special election to fill the remainder of the term.
"I went into the process wanting to make a difference, and I now leave knowing I did," Flaggs said. "Mississippi has been good to me."
He said he was able to learn aspects of government from each of the five governors — both Democrats and Republicans — he has served under.
Each governor from Ray Mabus to Phil Bryant has offered a set of unique skills from which Flaggs has drawn inspiration, he said.
"I've never had a governor I couldn't call on the phone," Flaggs said.