The British East India Company built the fort between 1713–1719. In 1714 Governor Collett obtained permission to build a new fort in Bencoolen. He named the new fort, which he built two miles from the older fort (Fort York), Fort Marlborough.
The fort was built on an artificial hill, and construction, using both convict and local labor, took several years to complete. During that period, the civil officers and the military garrison were divided between the old and the new fort.
In April 1715 Governor Collett sent a copy of the plan of the first Fort Marlborough; the plan showed that the fort was walled with earth ramparts and ditch, with gun platforms on the bastions. The pace of construction was slow.
In 1760, during the Seven Years’ War, a French squadron under the command of Charles Hector, Comte d’Estaing took the fort and used it as a base to attack and subdue other English settlements on the west coast of Sumatra. Before returning to the Mascarenes, he ransomed the fort back to the English.
At one time, the native people of Bengkulu burned the fort, forcing the inhabitants to flee to Madras. They returned in 1724 after an agreement was reached. In 1793, another attack on the fort occurred, killing one English officer, Robert Hamilton. Another attack happened in 1807, killing a resident, Thomas Parr. Both are commemorated with monuments in Bengkulu City erected by the British colonial government.
The British transferred Bengkulu, then known as Bencoolen, to Dutch control under the Anglo-Dutch Treaty of 1824, which defined British and Dutch spheres of influence.
After 137 years of British colonization, in 1824 Bengkulu was ceded to the Dutch East Indies in exchange for Singapore. In 1837, the fort had about 60 Dutch soldiers occupying it. The Japanese occupied the fort during their occupation of the Dutch East Indies (1942–1945). Then, during the Indonesian National Revolution period, the fort housed the headquarters of the Indonesian national police until the Dutch reoccupied the fort. When the Dutch left Indonesia in 1950, the Indonesian Army took over the fort. In 1977, the fort was handed over to the Department of Education and Culture to be restored and converted into a heritage site.