<p>The goby <i>Rhinogobius fluviatilis</i> follows an amphidromous life cycle characterized by hatching in freshwater stream areas, the subsequent dispersal of larvae to the sea, and upstream migration of juveniles for growth and maturation. The ability to acclimate to the diverse biotic and abiotic environmental conditions that vary along the river course represents a critical aspect of the life history strategy of this species, particularly in relation to their long-distance upstream migration. However, ecological factors causing the variation in the migration remain unclear. We hypothesized that migrating upstream provides fish with access to environments favorable for sexual maturation and growth because of factors such as water temperature and resource availability. We aimed to examine the migratory pattern and sexual differences in the amphidromous goby <i>R. fluviatilis</i> through field surveys. The observed patterns in body size and age structure along the river course revealed that this species continues migrating upstream beyond the juvenile stage. Furthermore, upstream migration patterns inferred from age composition along the stream differed between the sexes, with males initiating their upstream migration at an earlier time than females. In both sexes, some parameters related to sexual maturity and nutritional condition showed greater values at more upstream sites along the river, with sex-specific differences in the degree of the change. Overall, the lifelong continuation of upstream migration, as well as the sex differences in this migration, can be explained by the combined effects of ecological and physiological factors related to sexual maturation and growth.</p>