The Unai Emery tutored side will take on Valencia, who saw off Villarreal 2-0 on the night and 5-1 on aggregate.
On the other hand, Chelsea will face Frankfurt. The Blues survived a gallant effort from Slavia Prague to win 4-3 at Stamford Bridge and progressed 5-3 on aggregate.
Frankfurt scaled through on away goals. The German side lost 4-2 at Benfica but claimed a 2-0 win on their turf.
Below is the full Europa League quarter-final results…
Chelsea 4 – 3 Slavia Prague
Eintracht Frankfurt 2 – 0 Benfica
Napoli 0 – 1 Arsenal
Valencia 2 – 0 Villarreal.
Meanwhile, the semi-finals will be played on May 2 and 9, with the final in Baku set for Wednesday, May 29.