Rooney has scored plenty of goals in 2012 but did not pick up any trophies with his club and played a limited role at Euro 2012 for England, who were eliminated at the quarter-final stage.
The Red Devils were pipped to the Barclays Premier League title by local rivals Manchester City, who have three players on the list in Sergio Aguero, Mario Balotelli and Yaya Toure.
Robin van Persie, who was the league's highest scorer last term with Arsenal and joined Rooney at Old Trafford over the summer, is also included.
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.
A key man in Di Matteo's team has been recognised in former Chelsea striker Didier Drogba, as have seven members of Del Bosque's squad in Xabi Alonso, Sergio Busquets, Iker Casillas, Andres Iniesta, Gerard Pique, Sergio Ramos and Xavi.
The 2011 winner and Barcelona superstar Lionel Messi as well as runner-up Cristiano Ronaldo are also both shortlisted.
The winners will be revealed at the Fifa Ballon d'Or gala on January 7, 2013.