Although river-crossing structures can have a detrimental effect on the movement and distribution of anguillid eels (genus Anguilla), they have inhabited locations upstream of river-crossing structures in many rivers. However, the growth stage in which the eels start to climb river-crossing structures remains unclear. In this study, we directly observed, using infrared video camera systems, that the Japanese eel (Anguilla japonica) climbs a low-height vertical weir as a migratory barrier, confirming the ability of eels to climb over a low-height weir within a river. All eels climbed the weir at night, between sunset and sunrise. We observed that the total length of Japanese eels that climbed the weir ranged from 60 to 140 mm, suggesting that eels inhabiting the upstream area of a weir climbed it when they were small and then lived and grew upstream. Moreover, the general additive model showed considerable effects of water temperature and precipitation on eel climbing, suggesting that water temperature and precipitation are important for its activation. The results of this study also show the effectiveness of infrared video cameras in monitoring eel climbing, which could be applied to monitor fish migratory behavior through fish passages. The findings of this study are useful for the comprehensive management and conservation of wild eel stocks.