Azerbaijan and Armenia are in conflict over the Nagorno-Karabakh region and relations between the countries worsened in 2016 when at least 200 people were killed in clashes for which the Azerbaijan government has prohibited any Armenians from entering the country.
Back in 2015 when Mkhitaryan was with Borussia Dortmund, he had to again stay back in Germany for a Europa League tie against Gabala, another Azerbaijan side, because of security concerns.
And now with Arsenal's group stage game set to be scheduled for October 4 in Azerbaijan capital Baku, the attacker is expected to remain in London.
Arsenal coach Unai Emery however has now responded to the situation positively suggesting his side will reach out to authorities for a visa approval for the player and hope for a positive outcome.
"I would like that he can (travel) with us," Emery said.
"And this problem, if we can together arrange (a solution), it's better. But I have not yet spoken with him."
Regarding the situation, UEFA has assured the club that they will try to resolve the issue and released an official statement on the matter.
"It is a standard procedure for UEFA to send letters of support to associations, clubs or embassies in order to obtain visa for players in order to be able to travel to another country and play in UEFA competition matches," the governing body said.
Arsenal will face Qarabag in their second match in this season's Europa League where Emery and his players will make a 5,000 mile round trip in between Premier League matches against Watford and Fulham.