On 22 April 2016, Croatian Football Federation announced that the first stage of licensing procedure for 2016–17 season was complete.
For the 2016–17 Prva HNL, only seven clubs were issued a top level license: Dinamo Zagreb, Hajduk Split, Istra 1961, Lokomotiva, Rijeka, Slaven Belupo and NK Zagreb.
On 23 May 2016, it was announced that all remaining Prva HNL clubs were granted top level license.
Only two teams from Druga HNL acquired the top level license: Cibalia and Šibenik.
At the end of the season, ninth placed Cibalia qualified for a two-legged relegation play-off tie against Gorica, runners-up of the 2016–17 Croatian Second Football League.