Bouwmeester played in three World Junior Championships with the Canadian junior team. He became the youngest player to ever represent Canada at the tournament when he won a bronze medal at the 2000 tournament at the age of 16 years, 3 months. He recorded two assists in 2001 as Canada won another bronze medal. In 2002, Bouwmeester and the Canadian team won the silver medal, losing the championship game to Russia, 5–4.