As a member of the senior FR Yugoslavia national basketball team, Stojaković earned a bronze medal at the 1999 edition of the FIBA EuroBasket, which was held in France. He also won gold medals at the 2001 FIBA EuroBasket, which was held in Turkey, and at the 2002 edition of the FIBA World Championship, which was held in Indianapolis, Indiana. He also competed at the 2000 edition of the Summer Olympic Games. Stojaković was named the MVP of the 2001 FIBA EuroBasket, and he was also named a member of the FIBA World Championship All-Tournament Team at Indianapolis, in 2002. Joining him on that All-Tournament Team were fellow NBA stars Manu Ginóbili, Dirk Nowitzki, and Yao Ming, as well as New Zealand's Pero Cameron.