The 2016–17 Gamma Ethniki Cup is the 3rd season of the competition, since its official establishment in 2013, and the first to take place after the 2015–16 edition was not held.
In this competition, only the clubs of the Gamma Ethniki can participate.
In first round of the competition, the clubs in each group compete against each other in singles matches (overtime and penalties apply) until one club is declared Group winner.
However, all matches scheduled for 13 November were postponed via a direct order of the HFF, in association with UEFA and FIFA, in response to the arson of Superleague Chief Refereeing Officer Georgios Mpikas' house in Ierissos, Chalkidiki.
In the Second Round (Semi-finals), the four Group winners compete on neutral Ground on single knockout matches.