Intrinsic rate of natural increase (r) of certain species is important parameter in the analysis of population dynamics, thus have large impact on the estimation of stock status and future projection of the stock. We applied a two-sex age-structured matrix population model developed by Yokoi et al. (2017) to the estimation of r for shortfin mako (Isurus oxyrinchus) based on the life history parameter obtained in the Indian Ocean as much as possible. As a result of 80 combinations of life history parameter (sex ratio, litter size, reproductive cycle, sex-specific maturity age, sex-specific estimated longevity, sex-specific growth curve, sex-specific length-weight relationship, and estimator of natural mortality), median r was estimated to be 0.113 with a range of minimum and maximum values of 0.060 and 0.132, respectively. This estimate can be used as a prior which uncertainty included in each parameter was taken into consideration or re-estimated value based on selected parameter would be another candidate for the input parameter in the stock assessment model.