The France striker, who damaged stomach and groin muscles in his team's Champions League exit to PSV Eindhoven on Wednesday, should be ready for next season, Arsenal said.
"Thierry Henry will be out for a minimum of three months," manager Arsene Wenger told their Web site (www.arsenal.com).
"Unfortunately, this means he will now miss the rest of this season both domestically and internationally, but we are confident that he will be ready for the start of next season."
Henry has been dogged by a lack of fitness since returning from the World Cup in Germany, notably with a long-standing sciatic nerve problem, along with hamstring and foot injuries.
The latest setbacks have been the final straw and Arsenal will have to pursue their only remaining objective -- a fourth-place finish that would book them into the Champions League qualifiers -- without the club's record goalscorer.
Henry, who has also been the Premier League's top scorer for four of the last five seasons, leaves a side who are fourth in the table and look comfortably on course for that objective.
They are a point behind third-placed Liverpool but have two games in hand -- which they also hold over fifth-placed Bolton Wanderers, who are five points further back.
However, his absence will still be another blow suffered by a side which promised so much this season and in under two weeks have lost nearly everything.
CUP DEFEATS
Beaten in a stormy League Cup final on Feb. 25 by Chelsea, which led to bans for three of their players, Arsenal were knocked out of the FA Cup by Blackburn Rovers three days later.
Having reached the Champions League final last season, they could only make the last 16 this term, with Wednesday's 1-1 home draw with PSV resulting in a 2-1 defeat on aggregate.
The scoring burden will now fall on Togo striker Emmanuel Adebayor, one of the trio banned after the League Cup final and who had an extra match ban added by the FA on Friday to his automatic three-match suspension for a red card.
Dutchman Robin van Persie, Henry's original strike partner this season, has been missing since January with a broken bone in his foot and could be out for another two months.
On-loan Brazilian Julio Baptista, Frenchman Jeremie Aliadiere and England teenager Theo Walcott are the other forwards available.
Henry's absence will also be a blow for France's Euro 2008 qualifiying campaign.
France are second in Group B, trailing leaders Scotland on goal difference and two points ahead of the side who beat them in the World Cup final, Italy.
Ukraine are three points behind the French but have a game in hand, with the top two going through to the finals in Austria and Switzerland.
