The Belgium international is injured and is replaced by Asmir Begovic in goal.
Courtois reportedly injured his ankle playing basketball in a commercial shoot.
But Chelsea boss Conte refused to be drawn on how the goalkeeper was injured.
Antonio Conte has revealed why Chelsea star Thibaut Courtois is missing the Man Utd clash
"During the week he had an injury in his ankle," Conte told Sky Sports.
"He has not recovered in time for this game.
"I hope he is out for only this game.
Chelsea fans panic on Twitter as Thibaut Courtois ruled out of Man Utd clash Sun, April 16, 2017
Thibaut Courtois has been ruled out of Chelsea's Premier League clash with Manchester United due to an ankle injury, and Blues fans are worried
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Fans react as Thibaut Courtois is ruled out of Chelsea's clash with Man United
"I think it's not important now to understand the way he had this injury.
"The bad news is he is injured and now it is important to work and to recover very soon.
"Courtois is of course one of the best goalkeepers in the world but we have a lot of trust in Begovic to play a great game."
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