Centuries ago, a group of Tamil families migrated from the Padiya Kingdom and settled near Padmanabhapuram, the capital of Travancore. Some of them found employment in the Padmanabhapuram palace and worshipped Bhairavaswamy and Muttaraman, with Bhairava being a fierce manifestation of Lord Shiva. During this period, they decided to construct a temple dedicated to Lord Ganesha and collected contributions from the local families. While the temple was under construction, a pivotal family member had a divine vision (Swapna Darshanam) that revealed the presence of a black and white stone beneath a Venga tree in Veli Malai (part of Travancore at the time, now in the Kanyakumari district more of Tamil Nadu). This stone was meant to be used to carve a Ganesha idol. Following the guidance of this divine vision, they sculpted a Ganesha idol from the black stone and decided to consecrate it in the temple they were building. They invited the ruler of Travancore to preside over the auspicious occasion, and the temple was named Kulasekara Pillayar Temple. The street where the temple stands became known as Kulasekara Peruntheruvu. As the capital of Travancore later shifted from Padmanabhapuram to Thiruvananthapuram, many of these families relocated to Thiruvananthapuram due to their employment in the palace. Consequently, the regular daily rituals at the temple became irregular, prompting them to bring the Ganesha idol from Padmanabhapuram and place it in a family member's Bhajana madam in Puthenchantha, Thiruvananthapuram, where daily prayers continued. Later, the family decided to construct a shrine at the current location. The construction began with the foundation but faced financial constraints. They improvised by using cadjan, woven mats made from coconut palm leaves, for roofing and walls. During this challenging time, a devoted individual named Smt. Janaki Ammal, the wife of Sri. Ramachandraraj, donated Rs. 500, which enabled the completion of the present shrine. On the 15th Monday of Kumbha masam in Malayalam year 1109 (February 26, 1934), the Kumbabishekam, or consecration ceremony, took place. According to an inscription found on the idol, it dates back to the ancient civilization of Kulasekara Alwar Perumal, the seventh of the twelve mystic alvars. Due to its historical significance, a portrait of the idol was displayed in the Archaeological Museum for many years, gaining worldwide recognition. Sri Kulasekhara Pillayar is believed to have manifested in this temple as Sarvabista varadanayaka, bestowing blessings upon his devotees for centuries.