Muñoz was born in Santiago. In 1973, under the Salvador Allende government, he served as National Supervisor of the People's Stores (Almacenes del Pueblo) until the coup d'état of September 11, 1973. He holds a Ph.D. from Josef Korbel School of International Studies at the University of Denver, Colorado (1978), a Diploma in International Relations from the Catholic University of Chile (1975, graduated with honors), and also took courses at Harvard University. He received a B.A. with a major in Political Science at the State University of New York, Oswego. Recipient of the "Distinguished Alumnus Award" from the Graduate School of International Studies at the University of Denver (1991), he was bestowed with the title of Doctor Honoris Causa from the State University of New York (1996). He has received fellowships from: Resources for the Future, the Ford Foundation, the Tinker Foundation, the Twentieth Century Fund, and the MacArthur Foundation. He was a Ph.D. fellow at the Brookings Institution, Washington, D.C. (1977). He later taught at the University of Chile's Institute of International Studies.
He co-founded the Party for Democracy (PPD) and participated in the executive committee of the campaign to vote "no" on a second term for Augusto Pinochet during the 1988 plebiscite. During the administration of Patricio Aylwin, Muñoz was made permanent representative for Chile to the Organization of American States, (1990-1994) and ambassador to Brazil (1994-1998) during the government of Eduardo Frei Ruiz-Tagle. At the start of the administration of Ricardo Lagos, Muñoz was appointed Deputy Minister of Foreign Relations until January 2002, when he was designated Minister Secretary General of Government, a position from which he exercised considerable influence over policy, advising Lagos. He left the ministry in 2003, after being appointed Chile's ambassador to the United Nations, Permanent Representative. In May 2010, Muñoz was designated by UN Secretary General Ban Ki Moon as Assistant Secretary General, Assistant Administrator, and Regional Director for Latin America and the Caribbean of the United Nations Development Programme. In 2014, he was named Minister of Foreign Affairs of Chile by President Elect Michelle Bachelet.
Chile was elected a temporary member of the United Nations Security Council for 2003 and 2004, while Muñoz served as ambassador. Muñoz was chairman of a special UN committee on al Qaeda and Taliban sanctions, during which he noted a reluctance by many countries to cooperate in reporting names and information to the committee and in acting on information received by the committee. He was troubled by al Qaeda's continued ability to circumvent sanctions, which he said "need more teeth". In January 2004, Muñoz served as the President of the Security Council. He also headed up a panel to investigate the death of Benazir Bhutto at the request of Secretary General Ban in response to a petition for said inquiry by Pakistani President Asif Ali Zardari. That report was delivered in April 2010.
Most recent books: A Solitary War: A Diplomat's Chronicle of the Iraq War and Its Lessons, Fulcrum Publishing, 2008 (also in Spanish) and The Dictator's Shadow: Life Under Augusto Pinochet, Basic Books, 2008. Newsweek said about The Dictator's Shadow: Heraldo Muñoz has written "an insightful and poignant new personal memoir of the Pinochet years." The Washington Post stated: Muñoz has produced "a meticulous and vivid new book...Muñoz delivers a compelling, personal account of life in a police state and a strong reminder of how far Chile has come." The Washington Post listed The Dictator's Shadow among the best books of 2008. The New York Times featured Munoz's life and work in its Saturday Profile (November 15, 2008, pg. A6). Getting Away with Murder: Benazir Bhutto's Assassination and the Politics of Pakistan, W.W. Norton & Company, 2013, a book based on the aforementioned UN investigation over which he presided.