They were, however, one of the 11 winners of the 2006 UEFA Intertoto Cup, in which they defeated Spanish side Villarreal in the final round, only a couple of months after Villareal had played in the semi-final of the UEFA Champions League.
2. septembra tega leta so bili nogometni navdušenci širom Slovenije priča rojstvu rivalstva med NK Maribor in NK Olimpija.