Historians have found evidence that the original temple was built in 1248 in Kurukkal Valavu in Nallur at the same location of the present temple. Nallur was then the capital of the Jaffna Kingdom. But in 1450, Parakramabahu the 6th of the Kotte Kingdom, in response to the Arya Chakkaravarthi of Jaffna's to extend his rule to the South, sent his son Sapumal Kumara to bring the Jaffna Kingdom down to his rule. Sapumal Kumara defeated King Arya Chakkaravarthi, destroyed his palace and the original Nallur temple. But upon becoming Buvaneka Bahu the 6th , he sought to make amends by building a new temple in 1467 at a nearby location, says Shanmugapriya in Nallur Kanthaswamy: A Spiritual Experience.

And centuries later the Portuguese, after fighting witht the kings of the Jaffna Kingdom for more than hundred years, with the death of King Sangilian, captured it in 1620. The Portuguese General Phillip Oliviera used the Nallur temple as a fort.

During Dutch rule, the new temple was built in the same place in Kurukkal Valavu,as the original place.The main shrine has deity Vel, but later a statue of Lord Murugan was installed.

Further the Nallur festival of old days took place in the nights,with the procession carrying the deity preceded by women clad in shimmering outfits dancing to the beat of gigantic drums. The streets of Nallur were illuminated with flame of torches and lamps.