As per Hindu legend, during the churning of the Ocean of milk, a sperm fell at this place to originate as a "Naval" tree. It came to be known as Jambuvanam and over the period of several eons, a temple formed in the place.
The place thus came to be known as Navalur while presiding deity came to be known as Thirunavleesan.
As per another legend, Sukra (Venus) obtained the diving elixir that could bring back dead people. During the fight between Devas, the celestial deities and Asuras, the demons, Sukra helped the Asuras by bringing them back to life repeatedly. The Devas complained it to Shiva, who swallowed Sukra.
He then brought him back to life and installed him as one of the Navagrahas, the planetary deities. He also instructed him to help devotees based on the deeds.
Sundarar, an 8th-century saivite saint was born in the place and believed to have attained divinity by worshipping Shiva at the place.
The place is also believed to be the one where Adisesha got back his original colour attained on account of the poison. Brahma is believed to have worshipped the deity during Dvapara Yuga, while Sivapriyar, who went on to become Chandekeswarar worshipped the deity during Treta Yuga.

The main shrines of the temple
The original structure is believed to be existent from time immemorial, while the later additions are believed to have been built by Cholas, Pallavas, while the present masonry structure was built during the 16th century. As per inscriptions from the period of Parantaka I, there were seemingly three Shiva temples and one Vishnu temple in the place. One of the three, a Pallava temple named Kalinarisvaram, was destroyed by the locals. The inscriptions during the 32nd regnal year Parantaka I (recorded as 348 of 1902) mentions gifts to the Vishnu temple by Rajaditta-devar for perpetual lighting of the temple.

The other two Shiva temples are called Rajaditta Isvarattu Mahadevar temple and Agasteeswaram (recorded as 347 of 1902). While Agasteeswaram cannot be traced, Rajaditta Isvarattu Mahadevar temple (also called Rajaditta Isvaram) is the Bhaktajaneeswarar temple. The other inscriptions in the temple indicate the conversion of it to a stone temple from an earlier structure made of bricks. The inscriptions from Kannara-deva (Rashtrakuta Krishna III), mentions the Kannaradeva defeating the Cholas and death of Rajaditya during the Takkolam war.[2] There are inscriptions from later Chola emperors like Rajaraja Chola I (985–1014), Kulothunga Chola I (1070–1120) and Rajendra Chola III (1246–1279).[3] In modern times, the temple is maintained and administered by the Hindu Religious and Charitable Endowments Department of the Government of Tamil Nadu.

Shrines of the temple