His manager, Claudio Ranieri, presented the main award to France international Henry, whose 29 goals in 33 appearances have driven the Gunners to the Premiership title.
He was a clear winner ahead of fellow nominees Steven Gerrard, Frank Lampard, Jay-Jay Okocha, Alan Shearer and Patrick Vieira.
Arsenal captain Vieira said: "He will tell you it is a team game but he has been tremendous in the last two games when we have been a little bit tired and needed someone to do something special."
Henry said: "I am quite lucky to play in a special team. The strikers grab the headlines but I have special players around me. We play as a team and we are willing to fight for each other, and you need that ability.
"It's like we are a family, willing to do things together and fight for it."
Henry and Vieira featured in the PFA's Premiership team of the year which was dominated by Arsenal players with Lauren, Sol Campbell, Ashley Cole and Robert Pires also named.
Other London stars to be represented in the divisional awards were: Tim Cahill (Millwall), Michael Carrick (West Ham United) and Andrew Johnson (Crystal Palace) in the Division One team, and Gino Padula (QPR) in the Division Two team.
PFA team
Tim Howard . . . Man Utd Lauren . . . Arsenal Sol Campbell . . .Arsenal John Terry . . . Chelsea Ashley Cole . . . Arsenal Steven Gerrard . . . Liverpool Frank Lampard . . . Chelsea Robert Pires . . . Arsenal Patrick Vieira . . .Arsenal Thierry Henry . . . Arsenal Ruud van Nistelrooy . . . Man Utd
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