Boateng, who previously appeared for Hertha Berlin in the Bundesliga before a brief loan spell with Schalke's local rivals Borussia Dortmund, is expected to complete his return to Germany later on Friday.
The 26-year-old, who was born in Berlin but represents Ghana despite playing for Germany at youth level, was on target twice in AC Milan's 3-0 win over PSV Eindhoven in the Champions League on Wednesday night, which means he will be ineligible to appear for the Royal Blues in that competition.
Schalke were yesterday drawn against Chelsea, Basle and Steaua Bucharest in the Champions League group stage.
In Italy, former Tottenham and Portsmouth midfielder Boateng made 74 appearances for Milan, scoring 10 goals, many of which were spectacular efforts.
Perhaps his most newsworthy contribution in a Milan shirt, however, occurred in January when he walked off the pitch in protest after being racially abused during a friendly against Italian fourth-tier side Pro Patria.