In 2006, Nocioni started for Argentina at the 2006 FIBA World Championship. In a game against Venezuela, he landed on an opponent's foot, and it looked he injured his ankle, though he was cleared to play in Argentina's next game against Nigeria. In Argentina's game against Nigeria, Nocioni led the team in scoring, with 23 points, playing 18 minutes, while not missing a single shot. Nocioni was 9–9 from the field, including 5–5 from the 3-point line. "I don't think I've ever played a game where I didn't miss a shot - at least not for the national team." Argentina won group A of the tournament, going a perfect 5–0 in the first round of play.
Argentina lost to Spain in the 2006 FIBA World Championship semifinal, with a final score of 75–74. Nocioni had a chance to win the game for Argentina, but his three-pointer at the end of the game missed, giving Spain the win, and the chance to win the championship. Nocioni's Argentine team next played the US team in the bronze medal game, which Argentina lost 96–81. Nocioni scored 18 points in this game, in which he played against NBA teammate Kirk Hinrich.