The award is further recognition for the 24-year-old's outstanding campaign after scooping the Professional Footballers' Association and Football Writers' prizes last month.
Rooney scored 26 goals in 32 Barclays Premier League appearances, easily surpassing his previous best tally of 16, to help sustain United's title challenge until the final day of the season.
Rooney, despite a fitness scare after suffering a groin injury against Stoke on Sunday, is now expected to lead the England line at the World Cup in South Africa this summer.
Manager Fabio Capello is due to name his provisional 30-man squad for the tournament on Tuesday.
Rooney's latest award comes after it was revealed last week Tottenham boss Harry Redknapp had been made Barclays Manager of the Season.
Redknapp was recognised for his achievement in leading Spurs to a top-four finish.
The decisions were made by the Barclays Awards Panel, which includes representatives from football's governing bodies, the media and fans.