The Armenia international joined Manchester United in the summer from Borussia Dortmund, costing the club around £26million.
But he struggled to break into Mourinho's first-team in his opening months at Old Trafford.
Jose Mourinho pleased with Henrikh Mkhitaryan form
Henrikh Mkhitaryan scored Manchester Untied's third against Wigan
The 28-year-old made his first Premier League start on October 9 against Manchester City but was taken off at half-time and didn't feature again in the league until the end of November.
Mkhitaryan has since become a key player for Mourinho, getting on the scoresheet and picking up the man of the match award in yesterday's 4-0 FA Cup win over Wigan.
And Mourinho has been full of praise for the winger, who has scored four goals and provided three assists in his 19 United outings.
Manchester United's FA Cup player ratings against Wigan
Sun, January 29, 2017
Express Sport brings you Manchester United's player ratings from their FA Cup fourth round win over Wigan Athletic
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Sergio Romero – 7.1
"Since he came into the team, we and Micki himself thought he was ready," Mourinho said after the Old Trafford win.
"He had a good impact immediately, then he had a break with the injury against Tottenham, and then he came back and played quite well.
"So we are happy with him."