The Frenchman was widely expected to leave the Rossoneri in the summer, but has now inked a one-year extension with the Serie A club
The Frenchman's previous deal was due to expire on June 30 and reports suggested that the former Arsenal player would leave the Rossoneri on a free transfer.
However, the 28-year-old has now inked a one-year extension.
"Mathieu Flamini, who has been with the Rossoneri since 2008, will remain a Milan player next season. He has accumulated 100 appearances, and has won one league title and one Italian Super Cup," a statement on the Milan website reads.
Flamini joined Milan from Arsenal in the summer of 2008. He previously wore the jersey of Olympique de Marseille.