The 2016 CAF Confederation Cup group stage was played from 17 June to 24 August 2016. A total of eight teams competed in the group stage to decide the four places in the knockout stage of the 2016 CAF Confederation Cup.
<section begin=Draw /> The draw for the group stage was held on 24 May 2016, 14:30 EET (), at the CAF headquarters in Cairo, Egypt. The eight teams were drawn into two groups of four.<section end=Draw />
The eight teams, all winners of the play-off round, were seeded by their performances in the CAF competitions for the previous five seasons (CAF 5-year ranking points shown in parentheses): two teams in Pot 1 and six teams in Pot 2. One team from Pot 1 and three teams from Pot 2 were drawn into each group, with each team then assigned a random "position" in the group to determine the fixtures.
<section begin=Format /> In the group stage, each group was played on a home-and-away round-robin basis. The winners and runners-up of each group advanced to the semi-finals.<section end=Format />
<section begin=Tiebreakers /> The teams were ranked according to points (3 points for a win, 1 point for a draw, 0 points for a loss). If tied on points, tiebreakers would be applied in the following order (Regulations III. 20 & 21):
The schedule of each matchday was as follows.