The 24-year-old Manchester United and England striker topped the poll of journalists with just over 81% of a record number of votes cast, finishing ahead of Chelsea forward Didier Drogba and Manchester City's Carlos Tevez to win the prestigious accolade, which has been running since 1948.
Both United boss Sir Alex Ferguson and England manager Fabio Capello were present to watch Rooney, who led Manchester United's ultimately unsuccessful challenge to Chelsea for the Premier League title, receive his award at the FWA's gala dinner at the Lancaster London Hotel.
Rooney, who is recovering from a niggling groin problem, scored 34 goals in all competitions and is integral to England's World Cup hopes in South Africa.
The striker, however, has no intentions of resting on his laurels.
"I am only 24. Hopefully I can progress and the best years are still ahead of me," he said.
"I am always learning every day, and take things in from all my team-mates, both at United and with England.
"As a player you are never the finished article. I want to keep learning and getting better."
Rooney felt it was a privilege to follow in the likes of World Cup winners Bobby Moore and Sir Bobby Charlton to be named Footballer of the Year.
The striker admitted he could not see a future outside the game and revealed he intended to stay involved in the game for many years to come.
"I would like to [step into management]," Rooney said.
"I started doing my coaching badges this year, and probably did not do as many classes as I would have liked.
"Hopefully I can continue them next year.
"I love football and enjoy football - I can't see myself running a restaurant, I want to be in football."
Rooney's immediate attention, however, will now turn to the World Cup.
The striker has been struggling with ankle and groin problems since United's Champions League quarter-final first-leg defeat to Bayern Munich on March 30.
But now Rooney is focused on recovering full fitness and is relishing leading England's World Cup campaign in South Africa as Capello's squad aim to emulate the 1966 success.
England line-up in Group C in South Africa alongside Algeria and Slovenia and begin their campaign against the United States in Rustenburg on June 12.
Rooney added: "I am looking forward to the biggest tournament in the world and I cannot wait for that first game."
Preparations for the finals begin in earnest with friendlies against Mexico, at Wembley on May 24, and Japan, in Graz, Austria on May 30.
Rooney added: "I am looking forward to getting there with the lads and start the training for the game against Mexico and then it will be on to the World Cup."