The Borussia Dortmund star will leave the club at the end of the season as his contract expires, and he's been linked with a number of Premier League clubs, including Chelsea.
But Mourinho said he was surprised Chelsea were even mentioned as a possible destination for the Poland international.
"I think this story is a book that was written a long time ago," Mourinho told Sky Sport Germany as reported by Goal.com.
Speaking prior to Chelsea's match with German opponents Schalke, Mourinho continued: "Everybody knows how the story ends. It surprised me that he was even associated with us, it's that obvious."
Lewandowski has been heavily linked with Bayern Munich, and the striker confirmed today he's looking forward to a fresh challenge next season.
And Mourinho has seemed to suggest he agrees.
The Blues manager is expected to be in the market for a striker in the January transfer window having become frustrated by the lack of goals from his current first-team trio of Demba Ba, Samuel Eto'o and Fernando Torres.
The three Chelsea forwards have just two Premier League goals between them this season despite sitting second in the Premier League.