The name Cibalia comes from the Roman settlement called Colonia Aurelia Cibalae which was the precursor of the present-day town of Vinkovci.

The club was founded in 1919 as HGŽK Cibalia Vinkovci, and in 1925 the team merged with local rivals RŠK Sloga.

After the war re-established clubs Sloga and OFD Graničar merged and formed NK Dinamo Vinkovci which began competing within the Yugoslav football system.

The club was also penalized by UEFA in the same season with a deduction of six points for failure to fulfill financial obligations related to past player transfers.

Nevertheless, in the 2004–05 season, Cibalia outdid all of its opponents in the second league by a large margin, won the promotion playoffs and returned to Prva HNL.

It was in this season that they also had Croatian mixed martial arts legend Mirko Filipović play the final 8 minutes of a match vs HNK Vukovar.