Villianur's history stretches back over a millennium, with its most prominent early development occurring during the rule of the Chola dynasty. The foundation of the Sri Gokilambal Thirukameshwara Temple in the 12th century by Chola kings established the settlement as a vital center of Shaivite worship and community life in the region.
In the 17th and 18th centuries, Villianur was swept into the geopolitical struggles between European colonial powers and local rulers. It became a strategic location during the Carnatic Wars, a series of military conflicts involving the French East India Company, the British East India Company, and various Indian sovereigns. The town eventually fell under French colonial administration as part of French India. The French significantly influenced the area's infrastructure, local administration, and religious landscape. In 1876, French Catholic missionaries established the Shrine of Our Lady of Lourdes, introducing a strong Christian community that coexisted with the local Hindu population.
During the mid-20th century, Villianur played a role in the local movement for integration with the newly independent Republic of India. Along with the rest of the French establishments in India, Villianur was de facto transferred to the Indian Union on November 1, 1954, a date celebrated as Liberation Day in Puducherry. In its modern history, Villianur has transitioned from a quiet agrarian and temple village into a bustling suburban commune.