The 28-year-old Frenchman joined Everton in August 2022, making 32 appearances for the Blues and scoring one goal.
In the ongoing Premier League season, Maupay, who is in the final year of his deal at Goodison Park, has not featured in the first two games for Everton. The forward will join former Brighton boss Roberto de Zerbi in the French top flight. Marseille have also signed Mason Greenwood and Pierre-Emile Hojbjerg this summer.
Everton have secured the signings of Jake O'Brien, Iliman Ndiaye, and Tim Iroegbunam during this summer's transfer window. The Toffees are also optimistic about finalising a loan deal for 26-year-old Lyon midfielder Orel Mangala before the window closes.