The Swiss summer signing lasted just 24 minutes of Saturday's 1-1 draw at Augsburg after going down under a heavy challenge from Konstantinos Stafylidis.
Stafylidis was booked for the incident which saw Die Konigsblauen lose their record signing for the foreseeable future, with him not expected to play again this season.
The club confirmed the news following the match, wishing the former Basel man their best wishes in his recovery.
A statement on the club's Twitter page read: "Very unfortunate news: Breel Embolo will be out for some time with a broken ankle, sustained in today's game. Best wishes to Breel."
Schalke have been plagued by fitness problems so far this season, with most notably another summer signing Coke suffering a serious knee injury just a week after joining from Sevilla.