Edwardsiella tarda is a severe aquaculture pathogen that can infect many fish species and cause a systematic disease called edwardsiellosis, which can lead to high mortality under certain conditions. Currently, most vaccine candidates against edwardsiellosis are based on pathogenic E. tarda strains, which can be a concern in some cases. In this study, the vaccine potential of a natural E. tarda isolate, ATCC 15947, was examined in a Japanese flounder model. ATCC 15947 was found to be relatively avirulent to flounder but able to disseminate into and survive transiently in fish tissues following intraperitoneal (i.p.) injection. Fish vaccinated with ATCC 15947 via i.p. injection exhibited a high level of survival rate, which was increased to 100% by a booster injection. Fish vaccinated with ATCC 15947 orally in the form of alginate microspheres showed a moderate survival rate, while fish vaccinated with ATCC 15947 via the immersion route exhibited a low rate of survival. Following oral vaccination, ATCC 15947 could colonize transiently in the gut, liver, and spleen of the vaccinated fish. Both injection and oral vaccination with ATCC 15947 induced production of specific serum antibodies, the levels of which at different time points following vaccination were generally higher in fish vaccinated with ATCC 15947 via injection than in fish vaccinated with ATCC 15947 orally. Compared to control fish, fish vaccinated with ATCC 15947 showed enhanced serum bactericidal activity and significantly increased expression in genes encoding a number of immune-related factors. These results indicated that ATCC 15947 possesses good immunoprotective potential, which may be exploited in the development of E. tarda vaccines.