Tottenham appeared poised to sign the Anzhi Makhachkala forward after he completed a medical, but Chelsea now appear to be in pole position for the deal.
"I think he's already made his decision," Mourinho said.
The self-styled 'Special One' nodded in the affirmative when asked if that was Chelsea.
The BBC are reporting that the deal has been agreed and Willian will sign for £30m subject to a work permit hearing.
Mourinho added: "I don't like to speak before time because football can be crazy.
"I know what the player wants, so in this moment we cannot hide. That is a possibility."
Mourinho added that he preferred smaller squads "with 22 players", hinting that some players would lead.
But he said Juan Mata would not leave the club.
"He is a player we all like and all want to keep. We want more quality in the team, not less quality."