The Buddies’ former player and manager has been in the position since 2016 and always planned to stay on until retirement. He will stand down at the end of March.
He reflected on a “roller-coaster ride” between almost slipping into League One and establishing the Paisley side in its current position within the top flight.
He said: “Then last two years in particular have been an incredibly difficult time for us all, but we have made great strides at the club.
“Last season we reached the semi-finals of both the League and Scottish Cups for the first time since 1981/82 as well as achieving our highest top-flight league position since 1989.
“Fan ownership was achieved five years ahead of schedule with SMiSA taking over the majority shareholding on the club in July.”
Fitzpatrick, forever associated with the Saints, will remain in a matchday role at the club as ambassador and continue to support the team.
He added: “While I look forward to what retirement has in store, I will still be around the SMiSA Stadium to support the team. Come on Ye Saints!”
As a midfield player, he had two spells with the club, either side of two seasons at Bristol City and was part of the team when they lifted the 1987 Scottish Cup.
Fitzpatrick also had two spells as manager, succeeding Cup winning boss Alex Smith in 1988 and then stepping in to take over after Iain Munro’s brief reign in 1996.