Ellis ruptured his left anterior cruciate ligament in the Guinness Premiership semi-final against Bristol Rugby on May 5.
The England and Tigers medical teams and Harry have decided that surgery, which will take place later this week, is the best option for his long-term recovery.
England Head coach Brian Ashton said: "This is a major blow to Harry, to Leicester given that they are aiming for a treble with the Heineken Cup final and to England for the Rugby World Cup. Harry was a key figure for us in the RBS 6 Nations and he will be sorely missed. I wish him all the best for a full recovery."
Tigers Head Coach Pat Howard added: "This is obviously disappointing news for Harry, Leicester Tigers and for England. Harry has had an excellent season and an impressive Six Nations but now he will miss the Rugby World Cup and two big finals with Leicester. I really feel for him and we all look forward to having him back."