The 2016–17 EHF Challenge Cup was the 20th edition of the European Handball Federation's third-tier competition for men's handball clubs, which was won by Sporting CP running from 19 November 2016 to 27 May 2017.

All draws held at the European Handball Federation headquarters in Vienna, Austria.

Teams listed first played the first leg at home.

Teams listed first played the first leg at home.

Some teams agreed to play both matches in the same venue.