Herein, we compared the epidemiological aspects of pathogenic microbial foodborne disease (FBD) outbreaks in Korea and Japan from 2011 to 2015. In Korea, the cumulative incidence rate (CIR) of FBD was 12.6 per 100,000 individuals, and the patients per outbreak (P/O) was 22.1 for the period from 2011 to 2015. During the same period in Japan, the CIR was 17.4, and the P/O was 21.1. In Korea, outbreaks of FBDs were more common in summer, whereas those in Japan were more frequent in winter. In Korea, microbial agents accounted for 55.6% of all outbreaks, whereas that in Japan was 77.1% of all outbreaks. Moreover, Bacillus cereus, Clostridium spp., pathogenic Escherichia coli, Salmonella spp., and Vibrio parahaemolyticus were more common in Korea than in Japan. In summary, FBD outbreaks showed characteristic differences between Korea and Japan, reflecting differences in culture, food habits, climate, and geography between the two countries.