The first incarnation of NK Istra was NK Uljanik, a club founded by the Pula shipyard
Uljanik in 1948. The first club success was in 1959–60 when they qualified to the
Yugoslav Second League. In 1961 NK Uljanik merged with NK Pula to form NK Istra 1961. The club stopped functioning shortly thereafter, but was restarted by Silvano Faraguna and Ivan Čekić in 1964, when they played in the Pula county league. After the founding of an independent Croatia, the club played in the
Druga HNL between 1993 and 1998, when they dropped down to
Treća HNL. In 2001 they became the champions of Treća HNL and returned to Druga HNL. Two years later in the 2002–03 season, under the leadership of manager
Elvis Scoria, Istra played in the final of the
Croatian Cup, losing to
Hajduk Split. It is the only time, in the history of Croatian football, that a Druga HNL league club played in the cup final. In season 2003–04 the club was managed by
Igor Pamić. He managed to win the Druga HNL South, and beat
Međimurje (0–2, 2–0) in the play-offs, after penalties. The club played first league football for the first time in their history in the 2004–05 season, and managed their first Prva HNL win against
Osijek in the fourth gameweek. The club lost only one game at home, but failed to win a single away game. They finished tenth, and won the play-offs to remain in the first league. In 2005–06 the club president Gianni Rossando was replaced by Orsat Zovko. After a bad season start manager Pamić was replaced by
Milivoj Bračun. The new manager managed a streak of good results. In the second half of the season Bračun resigned from the managerial position and was succeeded by
Krunoslav Jurčić. The club finished in the season in seventh place. During the summer manager Jurčić was fired, and replaced by
Stjepan Deverić. Unstatisfied with the board, Deverić left before the start of the season.
Branko Tucak became the new manager. After a string of bad results and clashed with the players, he was replaced by Krunoslav Jurčić. Bad results, compounded with a poor financial situation threatened the club with shutdown. The intervention of the Istria govurner and arrival of new sponsors managed to save the club, while the new president became Darko Jergović. Pula finished the 2006–07 season in eleventh place, and lost the play-offs to
Zadar (3–0, 2–3). They would then return to the Druga HNL. Valdi Šumberac was appointed as the first manager. During this time, Istra was adopted by Demoni, who became the club's first group of ultras. At the end of August 2007 the club appointed Elvis Scoria as the new manager, while Šumberac remained as an assistant manager. Istra finished the season in the third place. However, the club finished the 2008–09 season as the champions of the Druga HNL and were promoted to the Prva HNL. Istra 1961 achieved their best domestic success in the 2013–14 season, when they reached the semifinal of the Croatian Cup. In June 2018, Istra was bought by the Baskonia-Alaves Group, who acquired the majority stake in the club, buying a total of 85% of the shares. On 14 April 2021, Istra 1961 repeated the success of the 2013–14 season, qualifying for the final of the
Croatian Cup, with a 3–2 home victory over
Rijeka in the semifinal. They fell 6–3 to
Dinamo Zagreb in the final. On 26 November 2023, Istra 1961 broke record for number of people attending their home game at
Stadion Aldo Drosina. The attendance were 8,606 people at the stadium that holds the capacity of 8,900. == Recent seasons ==