McGinn also picked up the Players' Player award at the event, sponsored by Universal Inspection (UK) Ltd, at the AECC.
Goal of the Season was won by Josh Magennis for his outstanding first touch, turn and finish against Inverness Caley Thistle in November.
Other players to pick up awards were Declan McManus (U20 Player of the Year) and Cammy Smith (Young Player of the Year), and Archie Knox collected a Special Recognition award.
"It was a very nice feeling to be the Player of the Year. I am over the moon to have won both the Players Player award as well as the one voted for by the fans. It is a great night for myself and it is the icing on the cake for what has been a very good season for me personally.
"The fans have been unbelievable towards me and I am very thankful to them for that. To win the award voted for by the fans means that you are doing something right on the park."
Asked about Magennis's award, McGinn replied: "I was more surprised at his first touch for the goal! No seriously it was an excellent finish by the big man and the award was well deserved.
"I would also like to congratulate Declan and Cammy on their awards as well," McGinn continued. "Both have had unbelievable seasons and both have been involved with the first team squad.
"For Declan to score 25 goals so far this season for the U20s is some achievement. To score 25 goals at any level takes some doing so I was pleased to see him getting recognised."
WATCH THIS! Niall McGinn's goals for the Dons this season:
See clips and interviews from the AFC Player of the Year Dinner on RedTV here