The news comes a big blow to Milan fans after the enforced scored a brace on Tuesday to propel to the group stages of the Uefa Champions League
Boateng was contracted to the Rossoneris until 2015 but after the European giants failed to offer him a new deal he has left the club.
He returns to Bundesliga where he started his career with Hertha Berlin before later joining Borussia Dortmund
The 26-year is eligible to play for Schalke at the Group stages of the Uefa Champions League as he has already played for AC Milan.
Boateng played 100 matches for Milan and scored 17 goals after joining the club in 2010.