The Gunners booked their place in the showpiece final on May 29 with a comfortable win over Spanish side Valencia on Thursday night.
Mkhitaryan only came on as substitute for Unai Emery’s side at the Mestalla but he could miss the final against their Premier League rivals later this month completely.
The Armenian missed Arsenal’s trip to Qarabag during this season’s group stage and the political strain between his homeland and Azerbaijan could mean he is unavailable again.
Back in October, the Gunners decided against trying to obtain the necessary international clearance in an effort to have the Armenia international available for selection.
Mkhitaryan would be required to apply to the Azerbaijani government for a permit to make the trip to Baku but Arsenal decided against going through the process.
The two countries have had no diplomatic relations since the Nagorno-Karabakh War, which ended in 1994.
Arsenal were adamant it was their decision not to take Mkhitaryan, with boss Unai Emery saying at the time:
‘He cannot travel here. My work is football.
‘I respect each person, I respect each culture, I respect each country. But I don’t know each situation in every country.’
In 2015, Mkhitaryan did not travel to Azerbaijan to face Gabala while with Borussia Dortmund despite being told by UEFA that he would get a visa.
Additionally, there would be considerable safety risks if Mkhitaryan were to go to Baku given his standing as one of the Armenia’s most high-profile figures and the historical bad blood between the two nations.