During the early seventies he briefly subscribed to Marxist ideology, and he headed Luis Echeverría's Center for Economic and Social Studies of the Third World during the mid-1970s.

Following Vicente Fox's election to the Presidency (representing a coalition of the National Action Party and the PVEM) on July 2, 2000, Aguilar served as the transition team's advisor on international affairs.

Following a speech to students at Mexico City's Ibero-American University on November 11, 2003, in which Aguilar claimed that the political and intellectual class of the United States sees Mexico as "a country whose position is that of a back yard" (patio trasero) and that Washington was interested in only "a relationship of convenience and subordination" and "a weekend fling" (un noviazgo de fin de semana), President Fox requested his resignation on 18 November.

The speech served as a pretext to fire him and placate the US, although Mexico never gave the US what it wanted: support for the 2003 invasion of Iraq.

After leaving the UN, Aguilar received an honorary degree from Ricardo Palma University (Peru) and hosted a weekly current-affairs show on television.