The knockout stage of the 2012 CECAFA Cup began on 3 December 2012 with the quarter-finals and ended on 8 December 2012 with the final. Matches were played at the Namboole Stadium and the Lugogo Stadium in Kampala, Uganda.
The knockout stage involved the eight teams which advanced from the group stage: the top two teams from each group and the two best third-placed teams.
In this stage, teams play against each other once. The losers of the semi-finals play against each other in the third place playoff where the winners are placed third overall in the entire competition and receive US$ 10,000. The winners of the final receive US$ 30,000 and the runners-up US$ 20,000.
The quarter-finals were played on 3-4 December 2012.