The 2012 AFC Challenge Cup qualification phase saw eight teams advance to the final tournament in Nepal. The qualification draw was held on 20 October 2010, in AFC House in Kuala Lumpur, Malaysia.
The seedings are based on the 2010 AFC Challenge Cup. Unlike previous editions with the exception of the inaugural edition, no team has been given direct entry into the 2012 AFC Challenge Cup. Defending champions Korea DPR, runners-up Turkmenistan and third-placed Tajikistan would now have to go through the qualifiers to enter the finals. The eight lowest ranked teams would take part in the playoff round while the remaining 12 teams would enter the Group Stage.
For the pre-qualifying phase, the eight lowest ranked teams played off over two legs on a home-and-away basis with the away goals rule, extra time and penalty shootouts to determine winners if necessary. The matches took place on 9 and 16 February 2011 with the four winners advancing to the group stage. However, for Afghanistan–Bhutan fixtures, they were rescheduled for 23 and 25 March and were played in at the Tau Devi Lal Stadium in Gurgaon, India.
The second leg of the Philippines–Mongolia fixture was originally due to take place on 16 February 2011. However, in early January 2011, Philippine Football Federation president Mariano Araneta said he wanted the match to take place at the same venue as the first leg on 12 February, citing the winter conditions in Mongolia.Mongolian Football Federation president Ganbold Buyannemekh insisted that the second leg be played in Mongolia but proposed a 15 March date instead as a compromise.