The Armenia international has made 10 starts in the Premier League this term and began the campaign as a key figure in Mourinho's plans.
However, his only appearance since November 5 was a 19-minute cameo off the bench against Brighton and Hove Albion 20 days later.
According to reports, Mkhitaryan and Mourinho were involved in a disagreement during a video analysis session, an incident which – coupled with a string of ineffective performances – fuelled mounting reports that the playmaker could be on his way to Inter.
But Mkhitaryan looks set to be brought in from the cold on Wednesday, when EFL Cup holders United take on Championship high-flyers Bristol City, with Mourinho also repeating his public explanation for the former Borussia Dortmund star's exile.
Speaking to reporters, Mourinho said: "We need to take the game really seriously, but I'm going to make a few changes and it's possible Miki [Mkhitaryan] is involved.
"In this moment we are playing with [Juan] Mata, [Jesse] Lingard, [Marcus] Rashford or [Anthony] Martial and [Romelu] Lukaku, and the bench has been Ibra [Zlatan Ibrahimovic] and one of the other ones - Martial or Rashford.
"There is no space for everybody because you need balance on the bench too."
Mourinho added: "I am making a few changes for the match, not many, because Bristol is one of the best teams in the Championship and for me now the Championship is not the Championship of five or 10 years ago."