Owing to numerous miracles attributed to the statue of the Virgin Mary in the church nearby, the fort was named as Fortress of Our Lady of Miracles of Jafanapatão (Fortaleza de Nossa Senhora dos Milagres de Jafanapatão).

[1] With the onset of the Sri Lankan Civil War, it came under siege on several occasions and was the scene of pitched battles.

From 1985 to 1995 it was under the control of the Liberation Tigers of Tamil Eelam (LTTE); during this time the LTTE destroyed several key features of the fort to stop the Army from gaining control due to the site being used to stage attacks, but it was recaptured by the Sri Lanka Army in 1995 after a 50-day siege during Operation Riviresa.

Today it remains garrisoned by a detachment of the Sri Lanka Army with limited access to visitors and is being renovated with Dutch funding.

[2] Buildings inside the fort include the governor's residence (King's House), Queen's House, Kruys Church, the Garrison Parade Ground, Police quarters and several buildings from the Portuguese era.