Alli, who has been left out of the last two games, has been linked with a move to Paris St Germain in recent days.
But he will travel to North Macedonia for the Europa League third-round qualifying clash against Shkendija on Thursday.
When asked if he expected Alli to stay, Mourinho said "yes".
After being substituted at half-time during the opening game of the season against Everton, Alli was not in the squad for the games against Lokomotiv Plovdiv or Southampton.
Mourinho said of his inclusion in the squad to face Shkendija: "I always told that he will have his opportunities.
"I always told that it is no problem at all to have him and, like every other player, performances are important.
"He is coming, he has a chance to play and it will be important to play, it will be important for him to perform."