The Welshman netted five goals across three appearances last month as the U23s extended their perfect start to the league season.
Three of Wilson's strikes came in a 4-2 victory over Tottenham Hotspur at Anfield while he also netted a brace in a 2-0 win against West Ham United.
And the 20-year-old's efforts in September have helped him see off competition from seven other nominees to clinch the Player of the Month prize.