The France international damaged groin and stomach muscles in Wednesday's 1-1 draw with PSV Eindhoven which saw the Gunners crash out of the Champions League.
As a result, the north London club have confirmed he will miss the next three months of domestic and international football.
The Gunners hope to have Henry back to full fitness for the start of the 2007-08 campaign.
Arsenal boss Arsene Wenger said: "Thierry Henry will be out for a minimum of three months.
"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."