To determine the actual status of the recruiting glass eel stock of Anguilla japonica, we conducted a continuous monthly monitoring program for 2 years between November 2009 and October 2011 at the Sagami River estuary, Japan. A total of 114 and 372 A. japonica glass eels were observed in the 2009–2010 and 2010–2011 seasons, respectively. Recruitment patterns were the same in both years, starting in early winter (December in 2009 and November in 2010), increasing slightly until March, decreasing in April, but attaining the largest peak in June, after which no glass eels were observed during August–October. The Japanese eel has been known to spawn mainly in the summer, and glass eels recruit to their freshwater growth habitats during the winter to early spring. Our results clearly demonstrate an unexpected late arrival of glass eels in the early summer for two recent consecutive year classes. The summer recruitment found in our study indicates the unusual phenology of the Japanese eel, which may be a possible response to recent climate change.