The Hong Kong Museum of History originated in the City Hall Art Gallery and Museum. It was founded in 1962 and was renamed the City Museum and Art Gallery in 1969. In 1975, it was split into the Hong Kong Museum of Art and the Hong Kong Museum of History. The latter was initially housed in rented premises in Star House, Tsim Sha Tsui. In 1983, it was relocated to a temporary site in Kowloon Park, and in 1998, it was moved to its present premises on Chatham Road South, Tsim Sha Tsui.

The permanent home of the Hong Kong Museum of History, with a gross floor area of 17,500 m², is housed in a new building constructed at a cost of HK$390M and funded by the Hong Kong SAR Government. It is a comprehensive state-of-the-art museum designed by the P&T Architects and Engineers Ltd., based on the architectural concept of Mr E. Verner Johnson. The new Museum and the neighbouring Science Museum together form a museum complex of a harmonious appearance and colour scheme.

Apart from the main museum at Chatham Road South, the Hong Kong Museum of History runs five branch museums, namely the Hong Kong Museum of the War of Resistance and Coastal Defence at Shau Kei Wan, the Lei Cheng Uk Han Tomb Museum at Sham Shui Po , Law Uk Folk Museum at Chai Wan, Fireboat Alexander Grantham Exhibition Gallery inside the Quarry Bay Park and Dr. Sun Yat-sen Museum in the Mid-Levels of Central.