Chukwuemeka scored Chelsea's only goal in the 3-1 defeat at the London Stadium in what was a bittersweet afternoon for the 19-year-old.
The goal was Chukwuemeka's first for Chelsea in 17 games since signing from Aston Villa last summer.
But the England u-20 international soon picked up a knee injury and did not return for the second half of the game.
An update on Chelsea's website says Chukwuemeka has had surgery and has begun a period of rehabilitation.
The statement read: "Carney Chukwuemeka sustained an injury to his left knee during our game against West Ham United on Sunday.
"Last night Carney underwent surgery and will now begin his recovery.
"The 19-year-old will work with the club's medical department on his rehabilitation at Cobham."
"Bitter sweet feeling scoring my first goal for Chelsea but picking up an injury and not coming home with three points," Chukwuemeka said.
"Minor setback but I'll be back very soon. Thank you Chelsea fans for your love and support."
Chelsea are next in action against Luton Town on Friday.
