The 2006 AFC Cup was the third edition of the AFC Cup, played by clubs from the Asian Football Confederation member nations.

Al-Faisaly from Jordan became the first side to win the competition two years in a row.

[1] The 'developing' 11 nations in the Asian Football Confederation were invited to nominate one or two clubs to participate in the 2007 competition.

2005 winners, Al-Faisaly qualify to the group stage.

Al-Faisaly (2005 AFC Cup winners & 2004–05 Jordan FA Cup winners) Al Ahed (2005 Lebanese FA Cup winners) Brothers Union (2005 Bangladesh Federation Cup winners) Mahindra United (2005 Indian Federation Cup winners) Merv Mary (2005 Turkmenistan Cup winners) Happy Valley (2005 Hong Kong FA Cup winners) Selangor FA (2005 Malaysian FA Cup winners) New Radiant (2005 Dhivehi League runners-up) Home United FC (2005 Singapore Cup winners)