The 26-year-old received the most votes from first-team squad members and collected his prize from Sir Alex Ferguson.
Despite injuries hampering his participation throughout the season, the winger was consistent when called upon and put in some fantastic performances.
"It's great that they've put their trust in me," said Valencia at the awards ceremony. "I'm very pleased that I have their support.
"It was tough not being able to go away and do a proper pre-season with the lads. But as the season went on, I managed to pick up and my fitness improved, and as a squad we've put in a good performance."
Sir Alex Ferguson also praised the winger, stating: "The form he's produced this season since coming back from injury has been amazing. He's a great professional and he has the qualities we love in our game. I think that's why the other players have given him this award.
"The most remarkable thing is the way he's come back from his injuries. He's a really good human being."
Valencia also picked up the Goal of the Season award for his effort against Blackburn in April, as well as the Supporters' Player of the Year accolade. And the Ecuadorian admitted his achievements would go some way to cushioning the blow of losing the Premier League title to rivals Manchester City on Sunday.
"I am very happy to receive all three awards," said Valencia.
"After last night, the longest night of my life, I will take heart from this.
"There should be 20 of these awards because all of my team-mates deserve one. I'd like to thank them and to thank my fans at home in Ecuador and Manchester United fans everywhere."
Valencia received 37 per cent of votes cast on the club's official website. Wayne Rooney finished as runner-up with 24 per cent and veteran Paul Scholes came third on 12 per cent.