In 1990 the team returned its traditional name of "Cibalia". The club spent much of the 1990s in the Prva HNL, Croatian top level. It remained in the Prva HNL until the 2003–04 season when it was relegated to the Druga HNL. 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.