Rooney was nominated for both the young player and senior player of the year awards, the senior award went to his bessie mate Steven Gerrard.
Cristiano Ronaldo was also nominated in the young player category and was named in the Premiership team of the year alongside Rooney.
PFA Chief Executive Gordon Taylor said: "Wayne Rooney's development under Sir Alex Ferguson has been great to see. For a young man he has got such strength and it is all allied to great skill and perception.
"He is also starting to show a lot more maturity too, which is pleasing to see and bodes well for Manchester United and
Rooney told reporters that he was ‘delighted to win the award:
"To win it twice on the run is a great honour and I am delighted with the award," said Rooney.
Rooney revealed that he had voted for Fabregas as Young Player and Thierry Henry in the senior award.
"I voted for Fabregas, but it was close between him and Darren Bent, who has been brilliant with all the goals he has scored for Charlton. But Fabregas has done really well for Arsenal.
"I also voted for Thierry Henry, for the goals he has scored and the overall performance - the main thing is that he was doing it all in the Champions League as well."