24 teams from 13 nations participated in the 2008–09 CONCACAF Champions League from the North American, Central American, and Caribbean zones. Nine of the teams came from North America, twelve from Central America, and three from the Caribbean. Below is the qualification scheme for the 2008-09 competition:
Teams in bold qualify directly for the Group Stage.
There was a two-legged Preliminary Round for 16 clubs, with the eight winners advancing to the Group Stage. They were joined by the other eight teams who were seeded directly into the Group Stage. The clubs involved in the Group Stage were placed into four groups of four with each team playing the others in its group in both home and away matches. The top two teams from each group will advance to the Knockout Rounds, which will consist of two-legged ties. The Final Round, to be held in late April 2009, were also two-legged. Also, unlike the previously contested CONCACAF Champions' Cup, the away goals rule is used in the CONCACAF Champions League, but does not apply after a tie goes into extra time.
The draw for the Preliminary Round was held on 11 June 2008 in New York City. The first legs of the Preliminary Round were played from 26 August 2008 to 28 August 2008, while the second legs were played from 2 September 2008 to 4 September 2008.
The draw for the Championship Round was held on 10 December 2008. In each round, teams will play their opponent once at home and once away. The four group winners from the Group Stage will play the second leg at home in the Quarterfinals. The order of the home and away matches for the Semifinals and Finals were determined at the draw.
In all rounds, if two teams are tied after both legs then two 15-minute halves of extra time are played. If the two teams are still tied on total goals after extra time a penalty shootout determines the winner.
The two-legged Final was played on 22 April and 12 May 2009. The second leg was originally scheduled for 29 April, but was postponed until 12 May by CONCACAF due to concerns over an outbreak of Swine Flu in Mexico.