For the majority of its existence between 1958 and 2010, the club was known as NK Varteks, honouring the name of its principal sponsor, a local textile factory.

However, after Croatia's independence in 1991 and the formation of the Croatian First Football League Varteks established themselves as one of the stronger sides in the new national top level.

Varteks spent the next 21 seasons in Croatia's top league, finishing third three times, and reaching the national cup final on six occasions.

During World War II, the club temporarily suspended operations and was then reorganised under the name of NK Tekstilac in 1945.

Serious financial troubles forced NK Varaždin into a period of bankruptcy, which eventually led to the suspension of the club by Croatian Football Federation before a scheduled 24 February 2012 match of the 2011–12 Prva Liga season.