In 1903, then Lt. Governor of Bengal initiated the idea of starting a small museum at Darjeeling to give visitors an opportunity to obtain information about birds and butterflies of the district. A suitable site was chosen in the Lloyd's Botanical Garden and a building was constructed at a cost of INR 14,000.00. To enable students to study the fauna of the hills a building was completed in 1915 at a cost of INR 50,000.00 The Bengal Natural History Society under the name 'Darjeeling Natural History Society' was formed in 1923 for management of the museum. Charles M. Inglis, an amateur ornithologist held the post of curator for twenty-six years from 1923 to 1948 and built up the museum with enthusiastic co-operation of E.O Shebbeare, Conservator of Forests, West Bengal; G.E Shaw, Superintendent of Cinchona plantation and a host of officials and tea planters. A journal of the Society first appeared as a quarterly in June, 1926, the above mentioned arrangement continued up to 1976. As the funds available were not enough, the museum was taken over by the forest department, Government of West Bengal in 1976. The publication fund was granted from the Hill Department Branch Secretariat from 1982 to 1991. After this the responsibility for publications was given to the Education Department, Government of West Bengal until 2001. His Excellence Shri Gopal Krishna Gandhi, the then Governor of West Bengal visited the old building of Bengal Natural History Museum on 07.06.2007. As per his suggestion a new museum was to be created at Padmaja Naidu Himalayan Zoological (PNHZ) Park. The construction of the building started in 2010 and was completed in 2013. Finally in 2015 the museum was shifted to a new building inside the premises of PNHZ Park, the new museum was opened to visitors on 23rd July 2016.
The display area in the new BNH Museum consists of five ecological zones namely Marine Ecosystem, Mangrove Ecosystem, Alpine Ecosystem, Lake Ecosystem & Wetland Ecosystem.; Migratory Birds; Entomological Section, Birds Section, Bottle specimens (Reptile, fishes, amphibians & mammalian infants), Mammalian section, Skull & skeleton section, Rolled specimens and Skin sections.

Birds:

BNHM has a collection of 371 bird specimens out of which 229 bird specimens are on display. The museum also has collection of bird's eggs (110 species) and bird's nests.

Mammals:

BNHM has a total 250 mammalian specimens out of which 51 mammalian specimens are on display for the visitors. There are 35 head mounts present in the museum. The prized collection is the taxidermy specimens of rare cats including golden cat, marbled cat etc., Red Panda, Himalayan Flying Squirrel, Clouded Leopard etc.

Reptiles and fishes:

BNHM has a total 46 bottle specimens of reptile & fishes.

Entomological section:

Butterflies, moths, dragonflies and beetles are well represented. Only a fraction of the total collection (moths and butterflies-608, beetles, dragonflies and other insects-1104) are displayed.

Reserved collection:

The museum also maintains 2922 rolled birds and 47 rolled mammal skin for study purposes. Apart from that, there are 52 well-maintained flat mammalian skins. BNHM has a taxidermy unit from its inception. This unit is manned by a trained taxidermist. Most of the small birds and mammals displayed here are cured, stuffed, and rendered ready for display.