The following year, Malhotra was named to the Canadian national under-20 team for the 1998 World Junior Championships, held in Finland. He was the second-youngest player on the team, behind Vincent Lecavalier. Malhotra was pointless in seven games as Canada was defeated in the quarter-finals by Russia, 2–1. The following year, he was not available for the tournament as he was playing in the NHL with the Rangers. However, in 2000, he was loaned to Team Canada by the Rangers' organization, as he was still eligible as a junior. Serving as team captain, he notched two assists over seven games in the tournament, held in Sweden. Canada earned the bronze medal, defeating the United States 4–3 in a shootout.