The Portugal international scored 42 goals in all competitions from United last season.
Players from more than 40 associations were involved in the voting process.
Ronaldo were joined by fellow United star Rio Ferdinand in the FifPro Team of the Year.
FifPro team:
Iker Casillas (Real Madrid), Sergio Ramos (Real Madrid), John Terry (Chelsea), Rio Ferdinand (Manchester United), Carles Puyol (Barcelona), Steven Gerrard (Liverpool), Kaka (AC Milan), Xavi (Barcelona), Lionel Messi (Barcelona), Fernando Torres (Liverpool), Cristiano Ronaldo (Manchester United).
