Chuayffet entered in politics in 1974 when he was appointed as delegate of Benito Juarez. In 1982 he was elected as Mayor of Toluca. In that same year he was appointed as Secretary of Education, Culture and Social Welfare of the State of Mexico, office that he hold until 1987.[4]
In 1993 he was elected as Governor of Mexico, taking office later on September 16. Two years later, in 1995 he was appointed by Ernesto Zedillo as Secretary of the Interior, he resigned in 1998 following the Acteal massacre.[5]
Since 1 December 2012 he serves as Secretary of Public Education.[8]
On 27 August 2015, President Enrique Peña Nieto named Aurelio Nuño to replace Emilio Chuayffet as Secretary of Public Education. Ill health following a gall bladder removal was speculated as the cause, since no explanation was offered.