During the colonial times, the strategic location of Poonakary Village drew the attention of several ancient Sri Lankan rulers. The fortress, Poonakary Fort or Pooneryn Fort, was established by the Portuguese in the 16th century to safeguard their possessions in Jaffna. The Dutch eventually gained control and fortified the fort, and in 1805 the British built a rest house at the fort. During the Sri Lankan Civil war, the fort became a centre of conflict between the Army and the LTTE (Liberation Tigers of Tamil Eelam).