Liverpool’s No. 24 held off competition from Gareth Bale and former Swansea teammate Ashley Williams to pick up the accolade.
The FAW awards, which are voted by journalists and broadcasters covering the 12 months from October 2011 onwards, were presented in Cardiff on Monday night.
Tottenham star Bale won the award two seasons in a row in 2010 and 2011, but was denied a hat-trick by Liverpool’s midfield ace.
It was also a double award for Allen, as he picked up Swansea City’s Player of the Year award for 2011-12.
“The last 12 months have been incredible for Joe and he’s made huge strides,” Wales manager Chris Coleman said. “He was born to play for a club like Liverpool and excel.
“I saw him grow up at Swansea. You could see the talent he had, and it’s brilliant that he’s showing just how much he has.
“He’s a great character, very humble, and someone who never gets carried away.”
Photo via Facebook/Joe Allen