The 23-year-old Belgium international will miss the champions' Premier League game at Everton on Saturday and the start of their Champions League group campaign.
Bosnian Asmir Begovic, signed from Stoke City this year, will replace Courtois who sustained the injury in training.
"I cannot tell you much but I can tell you he needs surgery in his right knee and will be out for quite a long time," Mourinho told reporters.
"The doctors have to be more specific but I think today we will be ready to give out more information.
"It is a big blow, it is not easy to have the best goalkeeper in the world injured but it's easy to have one of the best in the world to play and we have Begovic to play," Mourinho added.
"I'm very sad for Thibaut and the team but we have a top keeper -- Begovic will be in goal."
Chelsea, who sold long-time first-choice keeper Petr Cech to Arsenal in June, have made a disappointing start to the season, taking four points from their first four matches to fall eight points behind leaders Manchester City.
(Reporting by Ed Osmond; editing by Sudipto Ganguly)
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