A percoid fish from the middle Miocene freshwater beds of Iki Island, Nagasaki, Japan is described as a new species, Siniperca ikikoku of the family Sinipercidae based on three specimens. It is characterized by having 11 abdominal and 16 caudal vertebrae; 11 dorsal fin spines and 12 soft rays; three anal fin spines and eight soft rays; four large spines on the ventral arm and several short processes on the posterior margin of the preopercle; the first spine of the dorsal fin longer than half the second spine of the dorsal fin. This is the third known fossil species of the genus Siniperca and the second Miocene species of the genus. After the Miocene, fishes of Siniperca went extinct in Japan, because the large lakes and rivers disappeared in Japan. They were adapted to and dispersed in large rivers and lakes in China and Korea.