The devas and asuras worked together to churn the ocean of milk (parkadal) in order to acquire amrita, the elixir of immortal life. Mount Mandara and the serpent Vasuki played critical roles in the legendary Samudra Manthan, or churning of the ocean. Mount Mandara served as the churning rod, while Vasuki acted as the churning rope, wrapping around the mountain. As the devas and asuras churned the cosmic ocean to obtain the nectar of immortality, Vasuki endured immense physical strain and exhaustion from the arduous, zig-zag churning motion. To alleviate her fatigue and rejuvenate her energy, Vasuki sought solace in the worship of Lord Shiva. She retreated to this sacred site, taking refuge in a snake pit, where she performed her devoted Shiva puja, leading it to be known as 'Putrur'.

During the Pandavas' exile, Arjuna embarked on a sacred pilgrimage known as a "Theertha Yatra," journeying to various holy bodies of water. His travels eventually brought him to the revered site where the serpent king Vasuki had once worshipped Lord Shiva. Parched and weary from his long journey, Arjuna was overcome with thirst upon arriving at this hallowed place. It was then that Lord Shiva himself manifested before Arjuna, taking the form of an elderly man. The disguised deity handed Arjuna a stick known as a "dandam" and instructed him to press it firmly into the earth beneath the sacred Vagai tree, assuring him that water would spring forth. Before setting off to quench his thirst, Arjuna humbly requested that the old man to safeguard his precious sword until he returned. However, while Arjuna was away drinking the miraculous water, Lord Shiva mischievously hid the sword deep within Vasuki's snake pit before vanishing from sight. Upon returning, Arjuna was perplexed to find the elderly man and his cherished sword missing. With a flash of divine insight, he realized then that the old man was none other than Lord Shiva himself. The great god appeared once more before Arjuna and revealed the concealed location of the sword within the serpent's lair. This mystical encounter bestowed the name "Vaal Oli Puthur" meaning "the snake pit where the sword was hidden." As ages passed, this name gradually evolved into its current form, "Valaputhur." The sanctity of Valaputhur was further magnified when Lord Mahavishnu himself established and venerated a linga made of precious ruby at this very spot. Thus, the presiding deity of this holy place came to be known as "Manikka Vannar," in honor of the divine ruby linga worshipped by Mahavishnu.