Nallur Kandaswamy Temple lies about 1.5km from the Jaffna town on the Kankesanturai Road. This is one of the most important temples in the Jaffna Peninsula and the most well known. The history of the temple dates back to the time of King Parakramabahu VI (1411-1463) of Kotte Kingdom.
King Parakramabahu VI had two adopted sons, Sapumal Kumaraya (prince) and Ambulugala Kumaraya (prince). The king sent prince Sapumal to the north where the South Indian Vijayanagara Empire was trying to attach Jaffna. The prince successfully drove away the invaders killing the king Arya Chakravarti, and brought his wife and children to Kotte .
The King Parakramabahu VI appointed the Prince Sapumal as the regional ruler of Jaffna. It was this prince who built the Nallur Kovil for the Hindu people of Jaffna. Prince Sapumal later had to leave Jaffna to take over the Kingship of the whole island at Kotte . He was consecrated as King Buwanekabahu VI of Kotte. The Portuguese who captured Jaffna in 1560 demolished the Temple in 1621 leaving no traces of it. The temple then stood at Sankili Thoppu on the eastern side of the Point Pedro Road (The site was later used for erecting a Christian Church)
Jaffna again fell to Dutch in 1658. They were more tolerant on religious freedom and the temple was allowed to be rebuilt in the current location in 1734 by Don Juan Mappana Mudliyar as a humble temple dedicated to lord Murugan. The descendants of Mappana Mudliyar, who were the temple trustees, had taken the task of restoring the temple to its present splendour.