We undertook a comparative analysis of the epidemiology of reported human leptospirosis (HL) cases in Korea and Japan. Between 2006 and 2012, the cumulative incidence of HL in Korea was higher than that in Japan (1.26 vs. 0.14 per 100,000 population, respectively), and the total reported cases were 632 and 196, respectively. Significantly more men were infected than women in both Korea (63.0% men, P < 0.01) and Japan (87.8% men, P < 0.01). In both countries, the incidence was highest among those aged 40 years and older (60%), and peaked in autumn (78.5% cases in Korea, and 46.9% cases in Japan). However, Japan exhibited a significantly higher proportion of male cases, a younger age distribution, and less prominent seasonality. A significant difference was observed in the incidence of HL between the capital city and rural areas in Korea, but not in Japan. The differences in agricultural and forestry practices, and the efficacy or wastewater treatment infrastructure might influence the incidence level in rural areas in both countries. The differences between the 2 countries might be because of their unique geographical characteristics and variations in their levels of industrialization.