He was rector of National Autonomous University of Nicaragua at León (UNAN-León) from 1974 to 1980 and President of the Supreme Electoral Council from 1984 to 1996, overseeing the country’s first democratic transfer of power in 1990.

"[1] The university autonomy won by his father later facilitated Sandinista recruitment and organization of their primarily urban political cadre under the rectorships of Carlos Tünnerman (1964 to 1974) and Fiallos Oyanguren who became rector of UNAN-León, from 1974 to 1980.

[1][3] Fiallos Oyanguren was elected rector in a competition with his friend, the philosopher and jurist Alejandro Serrano Caldera.

[1] A member of the Sandinista National Liberation Front (FSLN), in 1990 he organized the elections for and ultimately oversaw Nicaragua’s first peaceful transfer of power, as his party’s candidate, incumbent Daniel Ortega, lost to Violeta Barrios de Chamorro.

[5] Antonio Lacayo, a Sandinista supporter who voted for Ortega but ultimately served as a central figure in the Chamorro administration, said later: “Without Mariano Fiallos [Oyanguren] there would have been no democratic transition in 1990.”[3] Fiallos resigned from the CSE in 1996, in response to the 1995 constitutional and electoral reforms, in which the National Assembly had established that members of political parties would make up the departmental and municipal electoral councils and the Voting Receiving Boards.