He has served in different posts at the Secretariat of Foreign Affairs. In 1991, he was Deputy Assistant Secretary for Inter-American Affairs and during that period he also represented Mexico at the Agency for the Prohibition of Nuclear Weapons in Latin America and the Caribbean (OPANAL). In 1993, he was posted to the Embassy of Mexico in Washington DC and was the Chief of Staff to the Ambassador, during the NAFTA negotiations. In 1995 he was put in charge of the office for anti-narcotics in the same diplomatic mission. In 2000–2003, Sarukhán was designated Chief of Policy Planning to the Secretary of Foreign Affairs, and served as Consul General in New York City in 2003–2006.