Mkhitaryan has played just 104 minutes of Premier League football this season since arriving from Borussia Dortmund in the close-season.
After problems with a thigh injury, he has been physically fit for a number of weeks but still unable to force his way into Mourinho's first team plans, even failing to make the bench in the midweek League Cup victory over Manchester City.
The Armenian International has not been involved since a harrowing experience in the home league defeat to City when he was substituted at half-time.
But despite the 27-year-old's tough introduction to life in English football, Mourinho still believes he will become an impact player in the Premier League and has no intention of parting company with him in the near future.
"Some players, with their profile, they are adapted to come and play, some others they need more time," Mourinho said on Friday. "Time to feel the intensity and the aggression, the game without the ball, the competitiveness.
The Manchester United boss continued, "Many times players come from different countries. The style of football is different and the reality is different for sure in terms of competitiveness. Mikhi needs time to become the top player he can be."
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Mourinho attempted to make a distinction between being physically fit and match fit in explaining why Mkhitaryan is struggling to stake a claim for a place.
But the United manager pointed to two similar examples as way of inspiration for how the midfielder can turn his Old Trafford career around.
"Willian, he arrived at Chelsea and had problems to play," said Mourinho. "He went through a process then after he became a top player, then the next season he became absolutely phenomenal and still is.
"When (Angel) Di Maria arrived at Real Madrid he also had to learn a lot about his game and a new reality.
"In Mikhi's case the process was interrupted by an injury that kept him out for about a month.” The former Real Madrid manager said, “To be out for a month in this process and then be fit but not fit to play you have to go through a process of getting match fitness then you need competitive level to do it.
"Of course we believe in him and of course we believe that sooner or later there will be no problem."
Another United midfielder, Michael Carrick, is also battling to earn a regular starting place in Mourinho's first-choice line-up.
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Mourinho, who has not handed a league start to the former England international this season, insists that the only problem he has with the veteran is that, at 35, he is coming to the end of his successful career, rather than the start of it.
"It's one thing to be 25, another thing to be 35," Mourinho said. "That's the logic of things. But the only thing I can say is he's phenomenal.
"I can't expect from Michael what I can expect from (Marcus) Rashford or (Ander) Herrera in terms of playing three, four, five, seven consecutive matches. But he's phenomenal and when he is on the pitch, he gives us important things, said the former Chelsea manager.
"He's not just a player, he is somebody who has a big understanding of the game and it's a pity sometimes you can't stop the clock. Of course, I wish he was 25."
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