Two rotavirus vaccines are currently available in Japan. We estimated the incremental cost-effectiveness ratio (ICER) of routine infant rotavirus immunisation program without defining which vaccine to be evaluated, which reflects the current deliberation at the Health Science Council in charge of Immunisation and Vaccine established by the Ministry of Health, Labor and Welfare of Japan. Three ICERs were estimated, one from payers' perspective and 2 from societal perspective depending on the scenarios to uptake vaccines. The health statuses following the birth cohort were as follows: not infected by rotavirus, asymptomatic infection, outpatients after infection, hospitalised after infection, developing encephalitis/ encephalopathy followed by recovery, sequelae, and death.