The Gokarn Shaka Math was established by P.P. Shreemad Jeevottam Teerth Shreepad Vader Swamiji, the third Guru in the lineage. While Bhatkal had served as a primary seat, the mid-16th century brought significant unrest to the coastal region. At that time, Bhatkal was a bustling port involved in international trade with the British, Portuguese, and Dutch. However, this wealth led to violent trade disputes. In 1542, when the Queen of Bhatkal refused to pay tribute to the Portuguese, Governor Afonso D'Souza attacked the port with 1400 warriors, burning dwellings and killing many civilians.

Observing this looting, arson, and the rising sense of insecurity among the people, P.P. Shreemad Jeevottam Teerth Shreepad Vader Swamiji made the visionary decision to shift the headquarters. They chose the calm and quiet spiritual atmosphere of Gokarn, near the holy Kotiteertha, to serve as the Central Matha for the benefit and safety of visiting disciples. They installed the idol of Shree Bhoo-Vijay Vitthala here, which they had brought from the Gandaki river.

Later, the Math was moved to its current location by the 6th Guru, P.P. Shreemad Ramachandra Teerth Shreepad Vader Swamiji. Significant renovations were performed in 1811 by the 16th Guru, P.P. Shreemad Lakshminath Teerth Shreepad Vader Swamiji, who also established the Maruti Gopura Mandir in 1813. The Math features sacred doorkeepers Jay and Vijay and the holy Vrindavanas of the 4th and 12th Gurus.