It owes its establishment to the fund-raising efforts of Sir Hugh Low and Sir Frank Swettenham, Resident of Perak from 1889 to 1895, Resident-General of the Federated Malay States (now Malaysia) in 1896–1901, and Governor and Commander-in-Chief of the Straits Settlements 1901–1904.

The museum was initially concerned with natural history particularly ethnography, zoology, botany and geology, all key areas of interest of its founder Sir Hugh Low.

Its first curator was Mr. Leonard Wray Jr., a botanist, geologist and Superintendent of Government Hill at Larut (1883 to 1903).

In the beginning, the museum was housed in some renovated government offices while the main building of Neo-classical design was under construction in 1883.

The building comprised an office, library and exhibition hall (Gallery A) and was only completed in 1886 due to lack of funds.