It is believed that the shrine's name is derived from the word 'kifune' (lit. Yellow Boat) and it is said that the 'Mifunegata-ishi' pebbles in the precincts of the rear shrine cover the boat on which Tamayoribime no Mikoto arrived.
社名の由来は「黄船」によるものとし、奥宮境内にある「御船型石」が、玉依姫命が乗ってきた船が小石に覆われたものと伝える。