In the 2003-04 season, the board was reconstituted with new members joining the club, with new sponsors. Their main objective was to create Zrinjski among the best club in Croatia before the 100th anniversary celebration in 2005. Zrinjski was then able to sign four players who were on loans from Dinamo Zagreb: Luka Modric, Marko Janjetovic, Ivica Dzidic, and Davor Landeka. Following the season, Dzidic and Landeka were able to stay on for the duration of the season. Even though Zrinjski was not at the top, the foundation for the following season was established. In the summer of 2004 Zrinjski signed some of the top stars in their league like Zoran Rajovic, Dusan Kerkez, Velimir Vidic along with Sulejman Smajic. The team, which was led by the manager Franjo Dzidic was crowned champions quickly, with a substantial advantage over the runners-up Zeljeznicar. Zoran Rajovic was top scorer in the league.
Many of Zrinjski's best players were on one-year contracts, and then left the team following the season. The team didn't perform well in the first half of the season. It was surprised to be eliminated from the UEFA Champions League first qualifying round by Luxembourg team F91 Dudelange. Zrinjski won the opening game away by 1-0, but was defeated at home in overtime, 4-0. After the first game in the league, Blaz Sliskovic was appointed manager.
Zrinjski finished the 2005-06 season in third place, earning a place in the Intertoto Cup, where Zrinjski knocked out Maltese team title="Marsaxlokk F.C. ">Marsaxlokk (3-0 home, 1-1 away) in the first round and lost to Israel team title="Maccabi Petah Tikva F.C. ">Maccabi Petah Tikva (1-1 away, 1-3 at home) at the end of the round.
In the 2006-07 season Zrinjski placed second and earned an UEFA Europa League place. The winter break was when Zrinjski dropped one of its most talented player Lamine Diarra who was transferred into Beira-Mar and then signed Zoran Rajovic, who was a star player in the past, as a free transfer. Zrinjski also made a deal with a former player - a veteran midfielder Mario Ivankovic from Brotnjo.
in 2007 and 2008, Zrinjski fell in the opening qualifying round against FK Partizan of Serbia 11-1 overall. But, Partizan was expelled from the tournament due to trouble with the crowd and Zrinjski advanced to the second round, where they lost 2-1 against FK Rabotnicki of Macedonia. In their domestic competition, they come in fourth place, but their victory at the Cup of Bosnia and Herzegovina brought them a spot in the UEFA Cup once again.
In the 2008-09 season Zrinjski achieved a 5-1 aggregate over FC Vaduz in the opening qualification round for the UEFA Cup, but lost 3-1 against SC Braga the following round. The team also took home their second Premier League for the second time, led by the talisman player Kresimir Kordic who scored the most goals with 13 goals in the league.
The title of league means that Zrinjski will be in an additional round in qualifying to the UEFA Champions League, just their second time participating in the tournament. However, they fell 1-4 in aggregate to SK Slovan Bratislava with a 1-0 home victory. An unsatisfactory 2009-10 season in the league put Zrinjski in fourth position.
Zrinjski's time in European football continued for longer during the season 2010-11 than other seasons, with the club winning both FC Tobol and Tre Penne before losing to Odense Boldklub in the third round of qualifying for the UEFA Europa League. Zrinjski was lower in the league rankings and was able to secure seventh place, meaning that the team would not be playing European football the following season. In the season of 2011-12, Zrinjski was able to improve just a little bit: a sixth-place finish meant the team would not be able to participate in continental football in the next season. In 2012-13, the season turned out to be one of the most difficult in the past 10 years. The team falling to a ninth place finishedfinish, however, they were able to be eligible for European football with a strong cup performance, and made it to the semi-final.
The 2013-14 season will remain in the hearts and memories of Zrinjski supporters. After a lengthy three-way race to win the title between themselves, NK Siroki Brijeg and FK Sarajevo, Zrinjski came with a victory to take home their third Premier League title, their first since 2004-05. The win over the title during the previous season again resulted in Zrinjski into an UEFA Champions League second qualifying round in which they were drawn against NK Maribor.
In the time from 2015 to 2018, Zrinjski had a dominant run in from 2015 to 2018 in the Premier League, winning three league titles in succession Two of them were taken with manager Blaz Sliskovic and the third from Vinko Marinovic. The club also improved in European competitions, playing in the third qualifying round in the UEFA Europa League in the 2018-19, 2019-20 and 2020-21 seasons. In the 2018 season, Zrinjski got eliminated in the third round by Bulgarian club Ludogorets Razgrad, in 2019, by Swedish club Malmo and in 2020 almost to be eliminated by Cypriot team APOEL. Incredibly, during the initial two European "campaigns" in the first two "campaigns" club was managed by Croatian managers Ante Mise and Hari Vukas respectively. In the third, Zrinjski was managed by Bosnian manager Mladen Zizovic.
After a disappointing season in 2020-21 season In the following 2021-22 season the club was named league champions for the record seven times under the direction of manager Sergej Jakirovic.