The Frenchman's influence on Arsenal's title-winning campaign made him the outstanding candidate.
He won ahead of fellow nominees Frank Lampard, who was second, Steven Gerrard (third), Alan Shearer, Jay-Jay Okocha and Patrick Vieira.
Chelsea midfielder Scott Parker was the surprise choice for young player of the year, beating his captain John Terry.
Henry's honour came just hours after Arsenal clinched the championship following a 2-2 draw at Tottenham.
He became only the third player to win it twice - after Mark Hughes and Alan
Shearer - and the first to win it two years running.
Arsenal had six players in the PFA's Premiership Team of the Year, which also included Vieira, Robert Pires, Sol Campbell, Lauren and Ashley Cole.
"I am quite lucky to play in a special team," Henry said. "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.
Gunners captain Vieira praised Henry's contribution to the their success, particularly in recent weeks.
"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," Vieira said.
Parker's emergence as a player with international potential was confirmed in
January when he joined Chelsea in a £10m move from Charlton.
He is not yet a fixture in the Blues line-up but started both legs of the Champions League quarter-final against Arsenal.
Parker said: "This is very pleasing for me and it rounds off a brilliant season, although there are a couple of things that could still go my way in the summer, such as the Champions League and the European Championship.
"It has been a tough year for me but a brilliant year. It was always going to
be tough leaving Charlton because I had not known anything else since the age of
nine.
"It was always going to take a bit of time to settle in at Chelsea but I
am happy with the way things are going."
Tim Howard (Manchester United), Lauren (Arsenal), Sol Campbell (Arsenal), John Terry (Chelsea), Ashley Cole (Arsenal), Steven Gerrard (Liverpool), Frank Lampard (Chelsea), Patrick Vieira (Arsenal), Robert Pires (Arsenal),
Thierry Henry (Arsenal), Ruud van Nistelrooy (Manchester United).
NATIONWIDE FIRST DIVISION
Robert Green (Norwich), Phil Jagielka (Sheffield United),
Danny Gabbidon (Cardiff), Malky Mackay (Norwich), Julio Arca (Sunderland), Tim Cahill (Millwall), Michael Carrick (West Ham), Jason Koumas (West Brom), Andrew Reid, (Nottingham Forest), Robert Earnshaw (Cardiff), Andrew Johnson (Crystal Palace).
NATIONWIDE SECOND DIVISION
Steven Phillips (Bristol City), Louis Carey (Bristol City), Graham Coughlan (Plymouth),
Danny Cullip (Brighton), Gino Padula (QPR), Carlos Edwards (Wrexham), David Friio (Plymouth), Brian Tinnion (Bristol City), Richard Wellens (Blackpool), Leon Knight (Brighton), Scott Taylor (Blackpool).
NATIONWIDE THIRD DIVISION
Chris Weale (Yeovil), Nathan Stanton (Scunthorpe), Andrew Crosby (Oxford), Efe Sodje (Huddersfield), Andrew Dawson (Hull), Peter Beagrie (Scunthorpe), Liam Lawrence (Mansfield), Michael McIndoe (Doncaster), Alex Russell (Torquay), David Graham (Torquay), Lee Trundle (Swansea).