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The present study investigated characteristics of the relative age effect (RAE) among a general sample of Japanese elementary and junior high school students. Japan applies a unique annual age-grouping by birthdates between April 1 and March 31 of the following year for sport and education. Anthropometric and physical fitness data were obtained from 3,610 Japanese students, including height, weight, the 50-m sprint, standing long jump, grip strength, bent-leg sit-ups, sit and reach, side steps, 20-m shuttle run, and ball throw. We examined RAE-related differences in these data using a one-way analysis of variance by comparing students with birthdates in the first (April–September) versus second (October–March of the following year) semesters. We observed a significant RAE for boys aged 7 to 15 years on both anthropometric and fitness data, but a significant RAE for girls was only evident for physical fitness tests among elementary school and not junior high school students. Thus, a significant RAE in anthropometry and physical fitness was evident in a general sample of school children, and there were RAE gender differences among adolescents.