The former Belgium international joined Monaco in October from Union Saint-Gilloise following the departure of Adi Hutter.
"AS Monaco announces the end of its collaboration with Sebastien Pocognoli at the conclusion of the 2025-2026 season," the club said in a statement on Monday.
"The club would like to thank Sebastien Pocognoli and his staff for their full commitment to AS Monaco and wishes them all the best for the future."
Monaco were fifth when Pocognoli took charge, but despite going on a 10-game unbeaten run they eventually finished seventh.
Pocognoli also guided Monaco to the knockout phase play-offs in the Champions League, where they were knocked out by eventual winners Paris Saint-Germain.