The origin of the National Agricultural University dates back to 1901, and during the administration of President EduardoLopezdeRomana, according to the study of the Belgian delegation that arrived in Peru in July of that year, the National Institute of Agriculture and Veterinary Medicine (ENAV) was planned and organized, consisting of engineers Jorge Vanderghem,Enrique Van Hoorde,Victor Marie and Juan Michel and veterinary Arturo Declerck.

An official inauguration took place on July 22,1902 as a department of the Ministry of Public Works, when he was Don Eugenio Larrabure Unanue Minister. The Central Agricultural Station was established in 1912 to develop agricultural experiments and serve farmers. Therefore, before the 15th anniversary, the College was already an entity implementing the three basic goals of the University: teaching, research and promotion.

First location assigned to the school was a pavilion in Fundo Santa Beatriz, where it worked for 30 years. In 1933, he moved to Valle de Ate La Molina estate and stayed there. The Public Education Act of 1941 gave higher education institutions the status of teaching, administrative and economic autonomy.

In 1960, the University Act 13417 granted university status to the National Agricultural College, known as the La Molina National Agricultural University.

In 1961, the following faculties became operational as academic institutions: Agronomy, Animal Husbandry, Institute of Agricultural Engineering and Research and Advanced Studies (now Graduate School). In the same year, the College of Science and the School of Economic and Social Sciences were established, later renamed the School of Social Sciences and later the School of Economics and Planning. The two colleges started working simultaneously in early 1962. In 1963, the Institute of Forestry Sciences, the Fisheries Institute in 1966 and the Food Industry Institute in 1969 became operational.

Subsequently, the Sierra, Selva and Forestales Institute was organized as a teaching and research centre covering areas related to several faculties that study specific issues.

The operational structure of the university regards departmentalization as an academic unit, as the core of the operation of research, teaching and social prediction, and brings together teachers of relevant disciplines under a flexible curriculum system.

La Molina National Agricultural University is governed by University Act No .23733, promulgated on 9 December 1983, reintroducing the faculty system, maintaining the academic sector and allowing each university to organize and establish its own academic system in accordance with its characteristics and needs.

Under the current university law, the governance of universities and colleges is exercised by university congresses, university councils, principals, college councils and deans.