The population of the botiid Parabotia curtus in the Katsura River, Lake BiwaYodo River system, Kameoka, Kyoto Prefecture, Japan, the only one recorded in the Kinki region since the year 2000, was subjected to a population viability analysis (PVA) based on demographic data between 2006 and 2013 (8 years). Count-based and age-structured models with several conditions for density-dependence, carrying capacity, migration rate, and bias in population estimation (48 settings in total) were used for calculating the quasi-extinction probability within 50 years (extinction threshold <10 individuals), using computer simulations. The estimated population for the 8 year period fluctuated from 200 to 2,300 individuals (average ca. 935, with a coefficient of variation of 66%). PVA demonstrated a significant extinction risk for this population (23–82% extinction in 45 of 48 settings). Although further population monitoring is necessary for a more precise evaluation, we conclude that this population faces a real extinction risk. Sensitivity analysis suggested several requirements for effectively enhancing population viability, i.e., restraining large biotic and abiotic environmental perturbations to avoid extreme depression of the recruitment of young, enhancing winter survival, and promoting upstream migration into the spawning site.