Maurizio Sarri’s side, who are still unbeaten in this season’s competition, was awarded a favorable tie against Slavia Prague at the ceremony in Nyon.
There will be an all-Spanish quarter-final draw between Villarreal and Valencia while Benfica and Frankfurt will go head to head for a place in the semi-finals of the competition.
The first legs will be played on April 11, with the second legs on April 18.
Chelsea will play the first leg at home first because both they and Arsenal cannot play in London on the same evening.
Should Unai Emery’s men make it through to the semi-finals of the competition, they will come up against the winner of Valencia and Villarreal while also being afforded a home game in the first leg of the last-four encounter.
The winner of Chelsea and Slavia Prague’s match will face either Frankfurt or Benfica over two legs for a place in the final.
Arsenal have won their only previous home game against Napoli in European competition, where they beat the Serie A side 2-0 in the 2013-14 Champions League campaign, with Mesut Ozil directly involved in both goals.
The German playmaker scored one and assisted the other in that match at the Emirates.
Meanwhile, the Blues, who haven’t lost in this season’s Europa League campaign, are unbeaten in their previous six games against Czech opponents in European competition, having won three and drawn three, while also managing to keep a clean sheet in four of the last five.