Juan played on Brazil's Copa América-winning teams in 2004 and 2007, also winning the FIFA Confederations Cup in 2005 and 2009. He scored the winning goal in the penalty shootout at the end of the 2004 Copa América Final against Argentina in Lima. In the quarter-finals of the same competition in 2007, he opened the scoring in a 6–1 thrashing of Chile in Puerto La Cruz.