Political tensions between Azerbaijan and the midfielder's native Armenia have persuaded Arsenal it is safer for him not to travel.
Arsenal have confirmed Henrikh Mkhitaryan will not travel with the squad to Baku to face Chelsea in the Europa League final.
Political tensions between Azerbaijan and the midfielder's native Armenia will see Mkhitaryan left out by head coach Unai Emery.
Mkhitaryan also did not travel to Azerbaijan when Arsenal faced Qarabag in the Europa League group stage last year.
"We have thoroughly explored all the options for Micki to be part of the squad but after discussing this with Micki and his family we have collectively agreed he will not be in our travelling party," said an Arsenal statement.
"We have written to UEFA expressing our deep concerns about this situation. Micki has been a key player in our run to the final so this is a big loss for us from a team perspective.
"We're also very sad that a player will miss out on a major European final in circumstances such as this, as it is something that comes along very rarely in a footballer's career.
"Micki will continue to be part of our preparations until we depart for Baku at the weekend."
Arsenal had previously questioned the decision to stage the Europa League final in Baku, given the high likelihood that the teams featuring in it would be from Western Europe. The Premier League club also registered a complaint about ticket allocations, with just 6,000 awarded to both Arsenal and Chelsea fans for the match in the 68,700-seater Baku Olympic Stadium.
Mkhitaryan: "It's the kind of game that doesn't come along very often"
Having considered all the current options, we had to take the tough decision for me not to travel with the squad to the Europa League Final. It‘s the kind of game that doesn’t come along very often for us players and I must admit, it hurts me a lot to miss it. I will be cheering my teammates on! Let‘s bring it home @arsenal #uel #final #arsenal #chelsea #afc #coyg
Mkhitaryan also acknowledged the decision to miss the May 29 final against Premier League rivals Chelsea with a post on social media.
"Having considered all the current options, we had to take the tough decision for me not to travel with the squad to the Europa League final," he wrote on Instagram.
"It's the kind of game that doesn't come along very often for us players and I must admit, it hurts me a lot to miss it. I will be cheering my team-mates on! Let's bring it home."
Mkhitaryan has made 11 appearances in Arsenal's run to the Europa League final, with a place in next season's Champions League at stake.
Arsenal have also expressed their