Alfaro also had a successful international career. As part of the Under-23 selection, he represented Mexico at the 1996 Summer Olympics in Atlanta, appearing in all four matches. He also collected 20 full caps for Mexico, including five qualifiers for the 1998 FIFA World Cup, and played on Mexico's title-winning squad at the 1998 CONCACAF Gold Cup. A favorite selection at the beginning of the regime of Bora Milutinovic, Alfaro gradually slipped down the pecking order with the emergence of Luis Hernandez and Cuauhtémoc Blanco as the preferred strikers under Milutinovic's successor, Manuel Lapuente. He collected his first cap against Bolivia in a 1–0 win at the Cotton Bowl in Dallas on 8 June 1996, and made his last international appearance on 18 March 1998, in a 1–1 draw with Paraguay.