The clubs were ranked according to points and tie breakers were in the following order: The seven group winners and the defending champion advanced to the quarter-finals.

The games were played over two legs, home and away; the team with the higher aggregate score was declared the match winner.

However, on 12 December 2007, the AFC awarded one to Thailand and the other one to Vietnam because the Indonesian domestic league and cup tournament wouldn't be completed in time for the start of the tournament.

Both Thailand and Vietnam therefore effectively recovered the entries they had lost the previous year.

The top scorers from the 2008 AFC Champions League are as follows: Gamba Osaka