The son of a Greek shipping magnate, Negroponte was raised in New York City and Long Island and attended the exclusive Phillips Exeter Academy in New Hampshire, graduating in 1956. He then studied at Yale University, receiving a bachelor's degree in 1960. That same year, after a brief time at Harvard Law School, he joined the U.S. Foreign Service. Negroponte was assigned to posts in Ecuador, Greece, Hong Kong, and Vietnam, and he later served as a deputy assistant secretary of state, first for Oceans and Fisheries (1977) and then for the Bureau of East Asian and Pacific Affairs (1980).

Negroponte was named U.S. ambassador to Honduras in 1981, at a time when Pres. Ronald Reagan (Reagan, Ronald W.)'s administration was engaged in covert military operations against left-wing governments in Central America. Negroponte's critics—including Jack Binns, his predecessor as ambassador—accused him of having ignored human rights abuses and the activities of death squads during his four years in Honduras. They claimed that Negroponte had aided the Contras, who were fighting against the government of neighbouring Nicaragua; Negroponte held that he had complained privately about the abuses while publicly supporting the newly elected government.

From 1985 to 1996 Negroponte held various key positions, including deputy national security adviser under Reagan and ambassador to Mexico (1989–93) and the Philippines (1993–96). He worked in the private sector until 2001, when Pres. George W. Bush (Bush, George W.) nominated him to serve as U.S. representative to the UN, where he helped build a case for war against Iraq, citing evidence of weapons of mass destruction; the evidence was later proved to be flawed (see Iraq War). In 2004 he accepted the job of ambassador to Iraq, where he was credited with reducing corruption within the U.S.-controlled administrative district of central Baghdad. The next year he was named DNI, a new cabinet-level position created at the recommendation of a congressional committee in the wake of the September 11 attacks (2001). The post was meant to centralize the leadership of the various U.S. intelligence agencies. Negroponte served as DNI for only a year, however, becoming deputy secretary of state in February 2007 under Secretary of State Condoleezza Rice (Rice, Condoleezza).