During World War II, Čakovec was occupied by Hungary so the club played in Hungarian competitions until the city was liberated in 1945.

In 1949, they were knocked out by Budućnost Titograd, suffering a 2–1 home defeat, and three years later they were crushed 7–0 by FK Sarajevo.

The club was again renamed NK Čakovec in December 1996, when it was bought by a group of local businessmen in order to save it from folding due to financial difficulties.

In the play-offs, played at a neutral venue in Velika Gorica, they failed to clinch promotion following a goalless draw against Jadran Poreč and a 2–1 defeat against Segesta.

The 1998–99 season saw the club missing promotion to the top flight after finishing fourth in the unified Croatian Second League.

However, they clinched their first top-flight point in their first home fixture of the season, being held to a 2–2 draw in a derby game against NK Varteks.

The team continued to deliver some good results during the autumn of 2000, including a goalless draw at home to Dinamo Zagreb, and even fought for a spot in the top-6 group, the Championship League, but eventually fell short by 5 points and finished the first part of the season in 7th place.

The team went on to start the 2001–02 season strongly, recording two wins in the opening two matches and topping the table on Day 2.

Playing in the Eastern Division of the Third League, they ended up being relegated to the fourth tier of Croatian football in 2008.