The Spanish right-back has been a key member of Atletico's defence in the Europa League, and has featured in every game that they have played in the competition so far, keeping three clean sheets.
However, he was forced to leave the field during the side's recent 0-0 draw with Real Betis in the 65th minute, after he picked up an injury.
22 April 2018
The problem was later confirmed to be a hamstring injury in his left leg, which will almost certainly rule him out of the two semi-finals, which are to be played on April 26 and May 3.
There is no confirmed return date, but Juanfran will aim to be back for the final of the tournament, if Atletico make it that far. Sime Vrsaljko is expected to take his place in Diego Simeone's side for the first leg of the Arsenal clash, which will be played at the Emirates.
Simeone will also be with out Diego Costa for at least the first leg, as the striker is sidelined with a hamstring injury of his own.