The 24-year-old has been included in the squad that will travel to Macedonia for Spurs' Europa League third qualifying round tie against Shkendija on Thursday despite reports linking him with a move to Paris Saint-Germain.
Mourinho said at a news conference on Wednesday that he does see Alli remaining at the club beyond the Oct. 5 transfer deadline.
"Tottenham is really a special club, my players must be special players and I must be a special coach because every club has situations where players are not playing, are on the bench, not selected," he said.
"And it looks like it is only for us that every time some player doesn't play or is not selected, it looks like something that doesn't happen in many other places. That is the first part of my answer, the second part is something we all know.
"Since Dele arrived from MK Dons, he had ups and downs. He had fabulous periods and also other periods where he disappeared from the top-level performances."
Alli has fallen out of favour at Spurs after being hauled off at half-time in the side's opening Premier League defeat to Everton. There were also reports he would be used to secure a move for Gareth Bale back to North London.
Bale ended up joining Tottenham on a straight season-long loan but questions remain about Alli, who has made 157 League appearances since a £5 million move from Milton Keynes Dons in February 2015.
"For me, it was not different than before," Mourinho said. "He had moments where he was so good and he also had moments where he was not so good and I think this lack of consistency when it happens in a player, the normal situation when you have other good players for similar positions, it is normal that when you are in great form, you play because you deserve, because your production is big for the team.
"When you are not in a good moment, you don't play, It is as simple as that. Players they have to prove on the pitch with their performances, they have to prove how good they are in that specific moment.
"Tomorrow he is selected, no decision yet whether starting or being on the bench. If he is on the pitch one minute or 90 minutes, he has to show us. That's simple."
Mourinho's relationship with Alli has been scrutinised as a result of interactions shown in the recent Amazon Prime documentary "All or Nothing: Tottenham Hotspur" in which he accuses the England international of being lazy in training.
"I always told [him] that he will have his opportunities," Mourinho said.
"I always told that no problem at all to have him and like every other player, performances are very important so he is coming.
"He has a chance to play and it will be important for him to perform. It will be important for him and every other player when the squad becomes competitive in many positions, it is important for every player that is on the pitch to have an answer and to perform.
"There is a tendency now when a player performs or doesn't perform, to give responsibilities on coaches. Some because the right love, some because they gave him the right stick. I always feel that 99% of the responsibility is the player. I have one percent, me and my staff and the people who work with the players, we have one per cent of the responsibility."