Rooney did not pick up any trophies with Man Utd, and played a limited role at the European Championships finals for England, who were eliminated at the quarter-final stage.
But the Red Devils striker remains a favourite of FIFA - who obviously don't put themselves out to check on players.
Manchester City have three players on the list in Sergio Aguero, Mario Balotelli and Yaya Toure.
Robin van Persie, who was the division's highest scorer last term, is also included.
The 2011 winner Lionel Messi and runner-up Cristiano Ronaldo are also both shortlisted.
Both United manager Sir Alex Ferguson and City boss Roberto Mancini have been nominated in the coach of the year category, along with Roberto Di Matteo, whose Chelsea side won the Champions League and FA Cup, and Vicente del Bosque, who guided Spain to the Euro 2012 title.
Player nominees: Sergio Aguero (Argentina), Xabi Alonso (Spain), Mario Balotelli (Italy), Karim Benzema (France), Gianluigi Buffon (Italy), Sergio Busquets (Spain), Iker Casillas (Spain), Cristiano Ronaldo (Portugal), Didier Drogba (Ivory Coast), Radamel Falcao (Colombia), Zlatan Ibrahimovic (Sweden), Andres Iniesta (Spain), Lionel Messi (Argentina), Manuel Neuer (Germany), Neymar (Brazil), Mesut Ozil (Germany), Gerard Pique (Spain), Andrea Pirlo (Italy), Sergio Ramos (Spain), Wayne Rooney (England), Yaya Toure (Ivory Coast), Robin van Persie (Holland), Xavi (Spain).
Coach nominees: Vicente del Bosque (Spain/Spain national team), Roberto Di Matteo (Italy/Chelsea), Alex Ferguson (Scotland/Manchester United), Pep Guardiola (Spain/Barcelona former coach), Jupp Heynckes (Germany/Bayern Munich), Jurgen Klopp (Germany/Borussia Dortmund), Joachim Low (Germany/Germany national team), Roberto Mancini (Italy/Manchester City), Jose Mourinho (Portugal/Real Madrid), Cesare Prandelli (Italy/Italy national team).
The winner of all the awards will be revealed at the FIFA Ballon d'Or gala on January 7, 2013.
Source: Newcastle United Mad