The Manchester United striker has scored 26 goals in 30 Premier League appearances this season and he follows team-mate Ryan Giggs in winning this award ahead of Didier Drogba, Cesc Fabregas and James Milner.
Aston Villa midfielder Milner has been rewarded for an excellent season and beat off competition from Rooney, Fabregas and Joe Hart to emulate club team-mate Ashley Young in winning this award.
Manchester United have four players in the Premier League Team of the Year, while Arsenal, Aston Villa and Chelsea have two apiece and Birmingham City are represented by Joe Hart.
Title winners Newcastle United are heavily represented in the Championship Team of the Year with four players, while Cardiff City and Nottingham Forest have two apiece.
Norwich City and Southampton both have three players in the PFA League One Team of the Year, while Charlton Athletic and Leeds United have two players in the team.
Notts County, Rochdale and Rotherham all have three players in the League Two Team of the Year, with Bury and Crewe Alexandra supplying one player each.