Rooney has scored plenty of goals in 2012 but did not pick up any trophies with his club and played a limited role at the European Championships finals 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 division'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 triumphant team has been recognised in now former Blues 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 Lionel Messi and runner-up Cristiano Ronaldo are also both shortlisted.
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).