The Nuclear Energy Commission was founded by the Resolution №389 of the Council of Ministers of the People’s Republic of Mongolia in 27 July, 1962. The Nuclear Energy Commission operated under Government of People’s Republic of Mongolia from 1991-1993, the Minister of Education and Science from 1993-1996, the Minister of Enlightenment from 1996-2000 and the Minister of Education, Culture and Sciences from 2000-2008.

Within the framework of the Prime Minister’s Administration, the Nuclear Energy Commission was re-established by the Resolution № 263 Government of Mongolia in 2008, and the Nuclear Energy Agency (formerly) implemented the Executive office functions from 2009-2014.   

The Parliament of Mongolia ratified the amendment of Law on Nuclear Energy in 2015, and the Government of Mongolia restructured the Nuclear Energy Commission (NEC) and formed its Executive Office based on the Order № 72 in 2015.