The French centre-back has had an injury-plagued career with the Blues and he has suffered yet another long-term setback.
Fofana sustained a hamstring injury prior to the Tottenham Hotspur game and he has now undergone an operation.
A statement from the Blues read: "The club can confirm that defender Wesley Fofana has today undergone successful hamstring surgery."
The former Leicester City man has been sidelined for the remainder of the season. He could make his comeback next term.
Fofana's regular injury concerns could force the Blues to enter the transfer market for a marquee centre-back this summer.
Benfica's Tomas Araujo was on their radar at the start of the season and the Blues could make a renewed approach this year.
The club have also been linked with Sporting CP's Goncalo Inacio, who is widely expected to pursue a new challenge.