In the 1998–99 season, Butyrskaya repeated as the European champion. She took silver behind Uzbekistan's Tatiana Malinina at that year's Grand Prix Final after falling twice in the long program. Butyrskaya then won gold at the 1999 World Championships, finishing ahead of defending World champion Michelle Kwan. She received all first place ordinals in both the short and the long programs at the event, landing seven triples in her long program and receiving seven 5.9s for presentation.