Before the establishment of the Natural History Museum (NHM), specimens collected by foreign scientific expeditions were allowed to be taken out of the country for lack of a proper repository facility in Nepal. As a consequence, much of the scientific research in the natural history of Nepal was done in other countries. Nepali scientists, students, and teachers had limited access to the information on their own country's natural inheritance. The museum was established in 1975 with the objective of serving as a research and education facility in Nepal for foreign and Nepali scientists, students and teachers. The museum was built on the premises of the former Ananda Kuti Campus. Today, it houses about 40,000 zoological specimens, 7,000 botanical specimens, 400 fossils and 100 skeletons.

The museum is open everyday, except on Saturdays and on official government holidays from 10 am to 4 pm.