Rooney, who has scored 34 goals for United in all competitions this season, took 80 percent of the votes cast by members of the FWA.
Chelsea striker Didier Drogba was a distant second in the voting with Manchester City's Argentine frontman Carlos Tevez in third position.
"I am delighted to win an award with so much history and tradition and to follow a long line of wonderful players who have been honoured by the FWA since 1948 gives me real pride," Rooney said.
"I would like to take this opportunity to thank my manager at United Sir Alex Ferguson, the coaching staff and my team mates without whose help and support this award would not have been possible."
Rooney, who was voted PFA Player of the Year on Sunday and also the Premier League's fans Player of the Season this week, has successfully filled the void left by the departure of Cristiano Ronaldo to Real Madrid although the tail end of his season has been interrupted by injury.
He is unlikely to play in United's final two Premier League games as they try and overhaul Chelsea at the top of the table because of a groin strain having recovered quicker than expected from an ankle injury.
"Wayne is a worthy winner of our prestigious award and the margin of his victory is testimony to the marvellous season he has had for club and country," FWA chairman Steve Bates said on announcing the award.
"His tally of 34 goals so far this season is certain to have captured the attention of our members but I am sure the overall improvement in his game at Manchester United has been of equal significance.
"Wayne's enthusiasm, hunger and desire mark him out as a special player and we hope he can carry his club form on to the international stage in the World Cup this summer and help England achieve their dream."
Rooney will be presented with his trophy in London on May 13.
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