Rooney ran out clear winner of the award, picking up 81% of the votes, well ahead of runners up Didier Drogba and Carlos Tevez.
"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 Football Writers' Association since 1948 gives me real pride," said Rooney.
"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.
"Also a big thanks to my family and friends for their constant support which is always appreciated.
"I thank the Football Writers' Association members who voted for me and I look forward to personally collecting my award at the Footballer of the Year dinner in London on May 13."