Bocanegra played for the United States at the 1999 FIFA World Youth Championship and earned his first senior cap for the U.S. on December 9, 2001, against South Korea. He became a stalwart for the team in 2003, solidifying his position during the 2003 Gold Cup and leading all defenders with thirteen appearances during that year. During World Cup qualification in 2005, his role with the national team became less clear, as he bounced between roles at center back and left back. On May 2, 2006, Bocanegra was named to the United States World Cup roster for the tournament in Germany. He started two of three games at left back during the 2006 World Cup.