Towards the end of World War II the club was founded on 26 April 1945 as the Fiskulturno društvo Zadar with the departments of football, basketball and athletics. On 9 February 1949, the football department was spun off as NK Zadar.
In 1992 as Zadarkomerc the club was founding member of the Prva HNL. Since then, the club has always played up to five seasons in the first division of Croatia. Since 2001, the club is officially named NK Zadar.
Their greatest success in the Croatian Cup was achieved in the 1995–96 season when they reached the semi-finals.
In 2001, the club was returned to Prva HNL, where he spent four consecutive seasons, but was again relegated after he was heavily defeated by Dinamo Zagreb at Maksimir (7-0), which the match ended at 62 minutes after the Zadar remained with too small number of players due to red cards and injuries of players.
After two seasons the Zadar has returned to Prva HNL on 30 May 2007 after beating NK Pula in the promotion playoff, 6-2 on aggregate.