The Armenia international would go on to miss Manchester United's next 11 games with Mourinho reluctant to give a reason as to why before he came off the bench in the 2-1 defeat to Fenerbahce last month.
A strong performance in last week's 4-1 win over West Ham in the EFL Cup, where he set up two goals, helped earn him a return to the starting XI in Sunday's 1-1 draw with Everton.
GETTY
Henrikh Mkhitaryan earned just his second Premier League start against Everton
GETTY
Mkhitaryan was subbed at half-time against Manchester City
And the 27-year-old is determined to hold on to his first team place.
"There was no bad relation with him [Mourinho], it was always good but the problem wasn't him, it was me," Mkhitaryan told Sky Sports News HQ.
"Now I understand why I have got my chance and I will keep it, I will hold it, because it is very important for me to play, to be a part of Manchester United.
GETTY
Mkhitaryan was keen to rubbish rumours of a rift between him and Jose Mourinho
Invalid email
We use your sign-up to provide content in ways you've consented to and to improve our understanding of you. This may include adverts from us and 3rd parties based on our understanding. You can unsubscribe at any time. Read our Privacy Policy
"I was thinking that I would be here as a starting line-up player but when I arrived I saw that there were 25 players fighting for their place and I understood that it wasn't going to be easy.
"I had a bad game against Manchester City but that is in the past so I kept working.
"I have done a great job to get my chance back and I think I did it a really long way until I start playing."