On November 15, 2011, Bocanegra joined the 100 cap club achieving his 100th international cap in a friendly against Slovenia. In March 2013, Bocanegra was initially included on the preliminary team for the start of the final stage of World Cup qualification; however, he did not make the final team. Bocanegra's further exclusion from qualification, in part due to his unstable club situation, led to the appointment of Clint Dempsey as captain of the USMNT. Bocanegra was subsequently not a part of the team at the 2013 Gold Cup or the 2014 World Cup.