In the late days of May, fullbacks Erjon Dushku and Dritan Smajli announced their departure from the club after terminating their respective contracts by mutual consensus.

[6] There, the club played for friendly matches respectively against Slovan Bratislava, Botoșani, MTK Budapest, Neftçi Baki and Universitatea Craiova.

Kukësi started its European campaign on 2 July in the match at Qemal Stafa Stadium against Torpedo-BelAZ Zhodino for the Europa League first qualifying round.

[10] In the returning leg one week later at Torpedo Stadium, Kukësi were able to hold off Torpedo-BelAZ Zhodino by gaining a goalless draw, despite the fact that Pejić missed a penalty-kick.

[15] In the returning leg at Podgorica City Stadium, Kukësi made history by overturning the 1–0 disadvantage to prevail 4–2, a match which was infamously marred by host crowd with their racist crusts.

[19] On the same day, Pero Pejić, the club's top goalscorer last season, left the team to join the Persian Gulf Pro League side Esteghlal for an undisclosed fee.

[24] Kukësi started its domestic season on 23 August with a 2–0 home victory against the newcomers of Bylis Ballsh thanks to the goals of Mateus Lima and Erick Flores.

[26] On the last day of the month, Kukësi brought the last reinforcements in the squad, signing Eglantin Dhima from Sopoti Librazhd, Franc Veliu from Flamurtari Vlorë, Enea Koliqi from Olympiacos Volou and Leomir Cruz from Marília.

[34] On 30 September, in the returning leg against Naftëtari Kuçovë, Kukësi was able to come back with a 4–1 home victory and a 5–4 win on aggregate to reach the second round of the Albanian Cup.

[42] On 4 November, in the returning leg of Albanian Cup second round, the team overwhelmed 3–0 Iliria Fushë-Krujë at home, securing an 8–1 aggregate victory and progression to the quarter-finals.

[48] The duo didn't make a decent debut in charge of the team as Kukësi suffered its second consecutive league defeat, this time at the hands of Partizani Tirana.

[61] Two days later, Nertil Ferraj joined the club on a free transfer following his departure from Teuta Durrës, signing a contract until the end of the season.

[67] In the first day of the new month, Kukësi signed with Kosovar defender Lapidar Lladrovci from Feronikeli and with Resul Kastrati from Teuta Durrës on loan until 30 June 2016.

[68] On the same day, Franc Veliu left the club after failing to make an impact in the team and joined on a free transfer to the rivals of Partizani Tirana.

[71] In the first leg of the Albanian Cup's quartar-finals, played on 17 February, Kukësi changed the face and overwhelmed Teuta Durrës 2–0 at the Zeqir Ymeri Stadium.

Back in Kategoria Superiore, Kukësi suffered another league defeat, this time to Partizani Tirana who won 1–0 at home thanks to the lone goal of Sukaj.

[77] On 2 April, Kukësi won three important points in their bit for a European spot after beating Bylis Ballsh 2–0 away thanks to the goals of Dvorneković and Erick Flores, both in the first half.

[78] Four days later, in the first leg of Albanian Cup's semi-final, Kukësi easily conquered Flamurtari Vlorë 2–0 at home thanks to the goals of Emini and Erick Flores.

[79] On 20 April, in the returning leg of Albanian Cup, Kukësi recorded another 2–0 win against Flamurtari, securing a 4–0 aggregate victory and progression in the final for the second consecutive season.