In ectotherms, life history traits such as growth rates vary in relation to the variation in environmental conditions. The ayu Plecoglossus altivelis altivelis is an amphidromous fish with annual life span, and it is widely distributed in Japanese Archipelago from Kagoshima to Hokkaido. Although growth rates and body size at upstream migration may play an important role to determine the later growth performance of this species, few studies have examined the geographic variation of those traits. In this study, we examined the otoliths of 74 adults collected from three rivers from high-, middle- and low-latitudes in 2017, in order to determine the growth rates and body size at upstream migration. Additionally, we examined those traits of subspecies P. a. ryukyuensis (n = 47), collected in 2016. In the early marine stage, high-latitude residents stayed longer at sea and entered rivers with larger body size. High-latitude residents experienced relatively low growth rates comparing with low-latitude residents at the marine stage, but in the late riverine stage, high-latitude residents maintained high growth rates while the other individuals reduced their growth rates. Previous study has reported that the length of the growing period at rivers determines the body weight after entering rivers, but high-latitude residents have shorter growing period (less than five months) in rivers than low-latitude ones (6–9 months). Considering this, high-latitude residents may increase their body size at mature in short growing period by keeping growth rates at high rate after entering rivers.