The 23-year-old has been struggling with a bruised foot since October, but was able to play 18 minutes in Saturday's 3-2 win over Wolfsburg.
However, he was not present in Tuesday's humbling 5-0 defeat to Chelsea in the UEFA Champions League due to the injury.
He is now set for a period on the sidelines after Schalke revealed the extent of the problem and the steps needed to return him to full fitness.
"Joel Matip will go into surgery to repair a hairline fracture in his right foot," a statement on the club's website read. "The procedure will involve the defender having a plate inserted into his right foot in order to close and secure the break.
"The Cameroon international will be unable to feature for Schalke until after the winter break.
"The 23-year-old will have to spend a couple of days in hospital after the operation and have a special shoe fitted to aid his recovery."
Matip, who represented Cameroon at the World Cup, has made eight appearances for Schalke this season, scoring two goals.