NK Čakovec experienced mixed fortunes in the Croatian Second League in the years following their relegation from the top flight, managing two 3rd-place finishes in the Northern Division of the league in 2003 and 2005. Following an 8th-place finish in the Northern Division of the Second League in 2006, they went on to play in the unified Second League in the 2006–07 season. However, they finished bottom of the 16-team league and were relegated to the Croatian Third League. Playing in the Eastern Division of the Third League, they ended up being relegated to the fourth tier of Croatian football in 2008.