Neuner returned as one of the favourites at the 2006 Junior/Youth World Championships in Presque Isle, Maine, United States, where she won two more titles (pursuit and relay) in addition to a silver medal in the sprint race. She did not participate in the 2006 Winter Olympics for the German team. At the World Cup in Kontiolahti in March 2006, Neuner achieved her first top ten finishes: she was fourth in the sprint and came in ninth in the mass start race.