The club was founded in June 2003 and started to compete in the Croatian Second League, where they replaced NK Omladinac, a club based in the Čakovec suburb of Novo Selo Rok. They finished top of the league at the end of the 2003–04 season, clinching promotion to the Croatian First League. They started their first season in the top flight with three defeats in their opening three matches, before beating Zagreb 1–0 on the road on Day 4 to clinch their first win of the season. However, they continued to experience very little success after that, only grabbing two further wins in the following 18 matches and being bottom of the table as the league split in two groups in March 2005. Their performance improved in the bottom-6 group, the Relegation League, where they had a streak of seven games undefeated and finished 5th, overtaking Zadar on the final day of the season. In their second top-flight season in 2005–06, they once again found themselves bottom of the table in March, although with 5 wins and only one point fewer than both Inter Zaprešić and Slaven Belupo. After three defeats in their opening three matches in the Relegation League, they managed a streak of seven games undefeated and overtook Inter Zaprešić after beating them on the penultimate day of the season. In 2006–07, they experienced mixed fortunes in their opening seven games, but then managed four consecutive wins and even found themselves in 4th place after Day 11. They eventually finished the season in 9th place, their best result in the top flight, with 11 wins in 33 matches. The 2007–08 season, however, brought very little success and they found themselves bottom of the table for majority of the season. They eventually finished rock-bottom, with only 15 points and mere three wins from 33 matches, 18 points behind the 11th-place Inter Zaprešić, and were effectively relegated to the Croatian Second League. In 2008–09, they finished fifth in the Croatian Second League, but were nevertheless directly promoted back to the Croatian First League for the 2009–10 season as the league was expanded to 16 teams and Slavonac CO, who finished above them, decided to withdraw from the top flight after failing to secure a proper stadium as their home ground. In the first half of the 2009–10 season, they performed well at home, recording 5 wins and 2 draws in 9 matches, but poor performance on the road saw them start the second half of the season in 13th place, just above the relegation zone. Despite winning two away matches in the second half of the season, a series of draws and defeats saw them dropping into the relegation zone with 6 matches left. A 4–1 defeat at Hajduk Split on the penultimate day of the season confirmed their 15th-place finish and relegation back to the second division. The 4–1 loss was later investigated for match fixing allegations.
Derby
In recent years Međimurje have contested the northern derby with NK Varaždin.
