Wat Sri Phan Ton was built by Phaya Phan Ton, the ruler of Nan from the Phu Kha dynasty, who reigned from 1960 to 1969. The name of the temple is derived from its founder, Phaya Phan Ton. At times, it has also been referred to as Wat Sli Phan Ton, with "Sli" meaning the Bodhi tree. In the past, there were large Bodhi trees on both the northern and southern sides of the temple, but they have since been cut down to make way for a road. Wat Sri Phan Ton received its ecclesiastical boundary from royal decree in 1962.