On 22 June 2005, Gilberto played in Brazil's 2–2 draw against Japan, in his only game of the 2005 FIFA Confederations Cup. His absence as a first team regular could be explained by his lack of games, and thus match fitness, for Arsenal during the season leading up to the tournament. Gilberto's appearance in the tournament gained him a winners medal, as Brazil went on to win the competition. On the back of his good Champions League form, Gilberto was selected for the Brazil national football team for the 2006 FIFA World Cup. Gilberto was substituted on in two games, and started twice due to another injury to Emerson. Brazil were beaten 1–0 by France in the quarter final. Following Brazil's World Cup disappointment, midfielder Juninho called for the older members of the Brazil squad (including Gilberto) to retire from international football. On the back of Gilberto's childhood idol Dunga being appointed Brazil coach, Gilberto did not take Juninho's advice, and subsequently continued his international career.