INTRODUCTION: The bone metabolism of male endurance runners during a competitive season has been little studied. Furthermore, Japanese runners have a special competitive season. This study aimed to investigate the change of bone turnover markers (BTMs) and other hormones in Japanese male endurance runners. MATERIALS AND METHODS: We investigated biochemical markers, bone formation and resorption markers and sex hormones, body composition using dual-energy X-ray absorptiometry (DXA), and training volume during a competitive season. 11 (age: 24.0 ± 4.3 years) Japanese male endurance runners were analyzed in this study. They participated in all measurements three times a year: the baseline (BL), the post-track period (PT), and the road race period (RR). RESULTS: Fat mass (FM) and percentage of body fat (% body fat) at RR (p = 0.009, p = 0.009) were lower than at BL. Specific bone alkaline phosphatase (BAP) decreased at PT (p = 0.004) and RR (p = 0.004) compared with BL. However, the bone resorption marker did not change. Free testosterone at PT (p = 0.032) was lower than BL. There was no correlation with blood variables and body composition or training volume. CONCLUSION: BAP and testosterone in Japanese male endurance runners decreased during the competitive season. However, there was no correlation between blood variables and training volume.