Freshwater eel Anguilla japonica is a commercially important species in East Asia. However, given the continuously decreasing resources due to many problems as climate change, habitat destruction and overfishing, mass seed production is crucial. In particular, the eel larvae present a unique life history, spending prolonged periods in the Pacific Ocean. Therefore, finding suitable feed that lasts through the long larval stages is rather difficult. In the present study, we histologically observed the development of digestive organs for 50 days after hatching (DAH). The endogenous reserves were completely absorbed at 7 DAH, and the first exogenous feeding started thereafter. The teeth appeared at 4 DAH and dramatically changed from needle-like to broad-based types by 50 DAH. The intestine remained as straight gut until 50 DAH. The intestinal cilia appeared first at 6 DAH and their density continuously increased thereafter. Interestingly, goblet cells appeared in the intestine, but not in the esophagus, where these cells are commonly observed in other teleosts. In addition, high amounts of eosinophil substances, assumed to be zymogen granules, accumulated in the pancreas, suggesting a specific digestive strategy of this species. Overall, these observations largely update the previous reports and can be useful to improve A. japonica seed production.