On 22 July 2016, Gjoka was appointed the new coach of Kukësi by signing a contract for the 2016–17 season. On 24 August 2016, Gjoka won his first trophy, the Albanian Superliga, beating reigning Albanian Superliga champions Skënderbeu Korçë 3–1. He was did not win his first Albanian Superliga game as Kukësi boss, as Kukësi stuck into a goalless draw away to Vllaznia Shkodër on 8 September 2016. On 7 June 2017, Gjoka agreed a contract extension, signing until June 2018.