Architectural and epigraphical features date the temple's foundational granite sanctum to the imperial Chola dynasty in the 11th century CE, during the reign of Rajendra Chola I or Kulothunga Chola. Over subsequent centuries, the temple received substantial architectural enhancements under the Pandya kings, the Vijayanagara empire, and Nayaka governors, who added the massive pillared halls and the eastern gopuram.
During the tumultuous colonial period of 1748, when the neighboring Vedapureeswarar Shiva temple was razed, the stone lingam and sacred idols were secretly relocated and sheltered within the precincts of Varadaraja Perumal Temple for several years, providing an extraordinary historical testimony to communal solidarity.
