The champions league was expanded to 35 clubs this year, with 5 teams starting from a knockout qualifying stage. An extra stage in the knockout phase was added so that the runners up as well as the winners from the group stage would progress. The previous season winner no longer got a bye through to the knockout round. Each team was allowed to field a maximum of four foreign players this season, one of whom had to be from an AFC Member Association country.
In the following table, the number of appearances and last appearance count only those since the 2002–03 season (including qualifying rounds), when the competition was rebranded as the AFC Champions League. TH means title holders.
The draw for the group stage was held on 7 January 2009 in Abu Dhabi, UAE.
Each club played double round-robin (home and away) against fellow three group members, a total of 6 matches each. Each team had been numbered from 1 to 4, the numbers determine the order of the fixtures.
Match Day 1: 1 vs 4, 3 vs 2
Match Day 2: 2 vs 1, 4 vs 3
Match Day 3: 1 vs 3, 4 vs 2
Match Day 4: 3 vs 1, 2 vs 4
Match Day 5: 4 vs 1, 2 vs 3
Match Day 6: 1 vs 2, 3 vs 4
Clubs receive 3 points for a win, 1 point for a tie, 0 points for a loss. The clubs are ranked according to points and tie breakers are in following order:
Greater number of points obtained in the group matches between the teams concerned;
Goal difference resulting from the group matches between the teams concerned; (Away goals do not apply)
Greater number of goals scored in the group matches between the teams concerned; (Away goals do not apply)
Goal difference in all the group matches;
Greater number of goals scored in all the group matches;
Kicks from the penalty mark if only two teams are involved and they are both on the field of play;
Fewer score calculated according to the number of yellow and red cards received in the group matches; (1 point for each yellow card, 3 points for each red card as a consequence of two yellow cards, 3 points for each direct red card, 4 points for each yellow card followed by a direct red card)
Drawing of lots.
Winners and runners-up of each group qualified for the next round.
^Sharjah were found guilty of fielding an ineligible player Abdelaziz Mohamed Al Mazam during the team’s AFC Champions League match against Al Shabab of Saudi Arabia on 8.4.09. Thus, Al Sharjah were fined USD 4000 and the match was awarded to Al Shabab 3-0. 
^Sharjah withdrew from the competition with two games remaining. Their results were expunged.
The draw for the round of 16 of the 2009 AFC Champions League was held on 7 January 2009, along with the draw for the group stage. The West Asian matches were played on 26 and 27 May. The East Asian matches were played on 24 June.
The draw for the quarter-finals and the remaining knockout rounds took place at Kuala Lumpur, Malaysia on 29 June 2009. The first leg matches were played on 23–24 September, with the second leg matches were played on 30 September.