Mourinho dropped his captain to the bench for Saturday's Premier League game against Leicester City following a series of lacklustre performances and United beat the champions 4-1.
"He didn't train yesterday, he did just a little bit of the session on Monday. He had a back problem," Mourinho told reporters.
"So I was completely convinced of playing him tomorrow from the beginning with this situation in the last couple of days, but I am not sure if I do that because of the situation you created with him," he added.
"Because I am here to protect him and not to put him in difficult situations I have to analyse whether the best thing for him is to start the game if he is not totally ready for it."
United suffered a surprising 1-0 loss to Dutch side Feyenoord in their opening group game, and Mourinho said victory on Wednesday was crucial if they are to progress to the latter stages of the competition.
"It is very important. We have to win. We have four matches after this and (if no win tomorrow) you have to win all the last four matches, which is difficult. So it is very important that we win the game," he added.
United full back Luke Shaw will miss the game at Old Trafford through illness but forward Anthony Martial has recovered from a calf injury.
Striker Zlatan Ibrahimovic, who retired from international football after Euro 2016, will lead the line for the hosts.
"We have two matches and then, for him (Ibrahimovic), it is two weeks without football," Mourinho said.
"He has to play tomorrow and then Stoke. Then he will have plenty of time to rest."
The former Chelsea boss also praised Juan Mata, who left Stamford Bridge to join United in January 2014.
"In my project at Chelsea he was a good player. In my project at Man United he is a very good player.
"We are trying to play in a different way. It is very adapted to his qualities. He has found a natural habitat for his football."
(Reporting by Nivedita Shankar in Bengaluru, editing by Ed Osmond)
