The museum was founded in 1918 by the Faculty of Sciences of the Universidad Nacional Mayor de San Marcos.

The first scientific expedition was organized by Rospigliosi in April 1918, that collected specimens of fauna, flora and minerals from the departments of Junín and Huánuco.

The second expedition was organized by the Geographic Society of Lima in 1920 that included the participation of Swedish geologist and explorer Otto Nordenskiöld.

In 1920, the rector of the National University of San Marcos, Dr. Javier Prado, interceded in order to acquire the collections of Antonio Raimondi for the recently created museum.

Highlights of the collections include: The first publication series was the Boletín del Museo de Historia Natural in 1937 aimed to divulge institutional activities and results of scientific research.