The Manchester United striker topped the poll of journalists with just over 81 per cent of votes cast.
Rooney, 24, finished ahead of Chelsea forward Didier Drogba and Manchester City's Carlos Tevez to win the prestigious accolade, which has been running since 1948.
The award is the England star's second of the season after he was named the Professional Footballers' Association Player of the Year last week.
He said: "I am delighted to win an award with so much history and tradition.
"To follow a long line of wonderful players who have been honoured by the Football Writers' Association since 1948 gives me real pride.
"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."
Ferguson meanwhile returned the compliment, revealing he thought the award was a foregone conclusion.
He said: "We expected that. It was a foregone conclusio
"I thought he would win both awards and deservedly so because he has elevated himself to a tremendous level now.
"He has brought maturity and authority to his game.
"It usually starts to show itself when young players move into their mid-20s and that is the case with Wayne now.
"Unfortunately the boy has had a couple of injuries recently but the season as a whole has been terrific."