Mkhitaryan also did not travel to Azerbaijan to face Gabala back in 2015 during his time with Borussia Dortmund.
Arsenal have defended their decision to leave Henrikh Mkhitaryan at home for their upcoming UEFA Europa League clash against Qarabag FK, as the Armenian would require a special visa to enter Baku.
The Daily Mail reports that due to diplomatic tensions between Armenia and Azerbaijan, Arsenal would need to apply for a special visa for the 29-year-old to take part in the game.
Qarabag manager Gurban Gurbanov has claimed that the Gunners were "afraid" of bringing the former Borussia Dortmund man into Azerbaijan's capital.
He said: "Arsenal tried to save this player but it is not a matter for us if he is coming or not.
‘If Henrikh Mkhitaryan would come to Azerbaijan it is not the first time — until now a lot of Armenian sportsmen came to Azerbaijan but it is the choice of Arsenal that they didn’t send him.
"Arsenal may be afraid that in front of 60,000 Azerbaijani fans, Mkhitaryan has some pressure and that is why they didn’t send Mkhitaryan."
I'm told Henrikh Mkhitaryan won't be making the trip to Azerbaijan for Thursday's game. Player's own decision based on the security situation amid the Armenia-Azerbaijan conflict. Could be an issue for the final in Baku as well if Arsenal make it that far.— Mattias Karén (@MattiasKaren) October 1, 2018
Mkhitaryan also did not travel to Azerbaijan to face Gabala back in 2015 during his time with Dortmund, despite being told by UEFA that he would get a visa.
However, Arsenal insist that it was their decision to leave the attacking midfielder in north London.
Gunners' boss Unai Emery remarked on the absence of his midfielder, saying: "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. For me, he cannot play.
"We are here, the players with the best mentality and preparation and possibility to play."
The 2019 Europa League finals are also set to be held in Azerbaijan, but Emery was coy when asked if Mkhitaryan would make the trip should Arsenal make it that far in the competition.
The Spaniard added: "It's a long time for us to arrive at the final. We are working to prepare for the next matches."
Gabon international Pierre-Emerick Aubameyang will also miss the trip due to illness, whilst contract misfit Aaron Ramsey will sit out the game as he is with his heavily pregnant wife.