Lukaku played a vital role as Antonio Conte’s side made it all the way to the final, losing 3-2 to serial winners Sevilla.
The Belgium international scored seven goals in six Europa League games after Inter Milan dropped down from their Champions League group.
Lukaku beat off competition from Sevilla’s Ever Banega and Manchester United’s Bruno Fernandes to claim the prize.
Lukaku told uefa.com: "I want to congratulate Sevilla personally. They won the competition so I congratulate them on having a great tournament.
"I want to thank Antonio Conte and his staff and everyone at the club - the board, the president - for their trust and for helping me through this season.
"My team-mates have been with me from day one. They're like brothers to me, they're real family members. Every day I come into training with a smile and it's because of them.
"I hope that this year we're going to do much better than we did last year and we're going to have a lot of success together."
Lukaku joined Inter from Manchester United last season and scored 34 goals in 49 appearances.
Last season Chelsea’s Eden Hazard, now of Real Madrid, won the Europa League player of the season.
