Pentapodus nagasakiensis has its dorsal fin supported by 10 spines and 9 soft rays while the anal fin is supported by 3 spines and 7 soft rays. The scales on the head extend forward to a level with the front edge of the eyes and the rear nostrils. The suborbital is not scaled and neither is the lower limb of the preoperculum. The pelvic fins are moderately long extending to or nearly to the level of the anus. The caudal fin lobes are of equal length and are pointed. The overall colour is yellowish shading to whitish on the lower body. There is a clear, wide yellow stripe running from the snout to the caudal peduncle with whitish stripes above and below it. This species has a maximum published total length of although standard length is more typical.