A Buddhist temple called Gokoku-ji was built alongside the shrine in 1367 by a monk from Japan's Satsuma province, creating an unusual blend of Buddhist and Shinto worship that lasted for centuries.

The shrine's name literally means 'above the waves,' and sailors entering Naha Port would look up at it from their ships to pray for safe voyages. The Ryukyuan kings themselves visited every New Year to pray for the entire nation's prosperity.

Originally a sacred site of Ryukyuan religion dedicated to nirai kanai (the mythical source of all life), the shrine was transformed into a State Shinto institution in 1890 after Japan annexed the Ryukyu Kingdom.

According to legend, a fisherman caught a mysterious glowing stone that brought him better catches. When the gods stole it back, an oracle appeared at that spot, eventually becoming the shrine known as Nanminsan.