Although Juninho had a period of prolonged domestic success during the 2000s, that contributed to him being considered as one of the best Brazilian players in the world at the time, he was not selected for the Brazilian squad that featured in the 2002 FIFA World Cup and in the 2004 Copa América missing both because of a recurring knee injury. Brazil would win both tournaments. He was however a member of the Brazil squad that won the 2005 FIFA Confederations Cup.