The history of Arulmigu Nainamalai Varadaraja Perumal Temple is deeply rooted in local legend and folklore. It is believed that the temple has existed for centuries, with various renovations and expansions carried out over time. The temple's association with Lord Varadaraja Perumal is central to its history, with stories passed down through generations about the deity's divine interventions and blessings. The temple has been patronized by various rulers and dynasties throughout its existence, contributing to its cultural and religious significance. While precise historical records are scarce, the temple's enduring presence and the devotion of its followers testify to its rich and vibrant past. It remains a living testament to the region's religious heritage.