The qualification stage consisted of three rounds, which were played as two-legged ties using a home-and-away system.

A total of 24 teams entered the draw for the first qualification round, which was held on Tuesday, 22 July 2015.

A total of 32 teams entered the draw for the second qualification round, which was held on Tuesday, 22 July 2015.

A total of 32 teams entered the draw for the third qualification round, which was held on Tuesday, 21 October 2015.

The draw of the EHF Cup group phase took place on Thursday, 3 December 2015, at 11:00 CET.

Because the French side HBC Nantes, the organizers of the Final 4 tournament, finished on top of their group they qualified directly to the final tournament and only the top three second-placed teams qualified to the quarter-finals.