In July 1995, the club, through mutual agreement with MNZ Murska Sobota, transferred to a different league system to compete in the MNZ Maribor leagues. Between the 1995–96 and 2000–01 seasons, Radgona competed in the Intercommunal Leagues organised by MNZ Maribor, before transferring back to MNZ Murska Sobota starting with the 2001–02 season. The club remained undefeated in the 2001–02 season in the 2. MNL (fifth level of Slovenian football) and earned promotion to the fourth tier after finishing top of the league. Radgona were promoted from the fourth tier in the 2002–03 season after finishing second behind Cven. After Cven withdrew from all competitions, Radgona were invited to play in the Third Division for the first time in their history. In their first third division season, they finished eleventh and got relegated to the lower tier. The season saw nine clubs relegate to the Intercommunal Leagues, because the 2003–04 Slovenian Third League consisted of four divisions (East, West, North and Centre), and for the following season the number of groups was reduced to just two (East and West). During their season in the third tier, their highest home attendance was 300 spectators watching the match against Beltinci on 16 August 2003. The club's highest win occurred on 6 September 2003 when they defeated Tromejnik at home with the score of 7–3.
