The 23-year-old beat Ademola Lookman to the honour despite the Nigerian firing Atalanta to the Europa League trophy after scoring a hat-trick in the final against Bayer Leverkusen.
Kudus had a great campaign in Europe and scored five goals in nine games as West Ham reached the quarterfinals of the Europa League.
Both Kudus and Lookman have, however, been named in WhoScored.com’s Europa League Team of the Season.
AS Roma goalkeeper Miles Svilar gets the nod between the ticks, while the back four of the Team of the Season is made up of Freiburg’s Ritsu Doan, Atalanta’s Berat Djimsiti, Sporting Lisbon’s Goncalo Inacio and Atalanta’s Matteo Ruggeri.
Kudus and Looman occupy either flank, with Bayer Leverkusen duo Florian Wirtz and Exequiel Palacios picked in the middle of the park.
Liverpool’s Cody Gakpo and Olympique Marseille’s Pierre-Emerick Aubameyang lead the Europa League Team of the Season as strikers.
Meanwhile, confirming Kudus as their Europa League Player of the Season, WhoScored.com said: “With a WhoScored rating of 7.57, West Ham star Mohammed Kudus is our Europa League Player of the Tournament.
“The Ghanaian attacker notched a total of five goals in nine games, with three of those coming against Freiburg in both the group stage and round of 16. Kudus also made 18 successful dribbles and 13 key passes across the campaign.”
Kudus enjoyed a productive debut season in the English topflight and was the first player in Europe’s top five leagues to record a hundred take-ons in the just-ended season.
He was also involved in 14 goals and six assists for the Hammers, including a spectacular overhead kick against Manchester City on the final day of the season.
The Ghana international’s impressive solo goal against Freiburg in the Europa League was also adjudged as West Ham’s Goal of the Season.