The Lei Yue Mun Fort was built by the British in 1887, positioned to defend Victoria Harbour's eastern approaches against naval attack. The Redoubt, the fort's core military structure, was completed that year. The Central Battery followed — its main display piece is a 7-inch RML Mark I gun weighing 4.5 tons, dating from the 1870s. The Western Battery mounted two 9-inch muzzle-loading guns, one of whose barrels was later recovered from the Admiralty Garden site in 1990 and weighed 12 tons. Between 1892 and 1894, engineers hewed the Brennan Torpedo station directly out of the rock of the headland — the last such station constructed anywhere in Britain or its overseas possessions. These were serious weapons for a serious strategic problem: defending a harbour that had grown into one of the world's most valuable trading ports.

Japan attacked Hong Kong on 8 December 1941, the same day as Pearl Harbor. The New Territories fell quickly, then Kowloon. British forces pulled back to Hong Kong Island and reinforced the Lei Yue Mun defences, trying to prevent the Japanese from using the narrow channel as a crossing point. The defenders repulsed several attempts, but on 18 December — under cover of darkness — Japanese troops crossed anyway, landing on the northeastern shore. By 19 December, the fort had fallen. The colony surrendered on Christmas Day, 1941, after 18 days of resistance. The fort's post-war life was quieter: a training ground for British forces until 1987, when it was finally vacated. The weapons that had failed to stop an invasion spent the next few decades pointing at an empty harbour.

The museum opened on 25 July 2000, after the Urban Council decided in 1993 to convert the fort rather than demolish it. The permanent exhibition, titled "600 years of Coastal Defence," traces the history of Hong Kong's shores from the Ming dynasty through the First and Second Opium Wars, through the Japanese occupation, and into the post-handover era. The casemates inside the Redoubt became exhibition galleries. A Historical Trail winds through the outdoor military structures. The total museum area covers 34,200 square metres. Super Typhoon Mangkhut closed the museum in September 2018 for four years of repairs; it reopened on 24 November 2022, structurally restored but historically unchanged.

On 3 September 2024 — the anniversary of Japan's surrender in World War II as commemorated in China — the museum was renamed. It was no longer the Hong Kong Museum of Coastal Defence. It became the Hong Kong Museum of the War of Resistance and Coastal Defence. The addition was deliberate: a new gallery now hosts regular exhibitions on China's War of Resistance against Japan, developed in partnership with cultural institutions on the mainland. Museum officials stated that the roles of British and Allied forces would not be diminished in the existing displays. Whether the balance holds in practice is a question visitors can assess for themselves. What is clear is that the fort, which once defended Hong Kong for the British Empire, now tells a story in which that defence is one chapter among several.