The increasing prevalence of childhood obesity is a global health issue. Past studies in Japan have reported an increase in both body mass index (BMI) and risk of obesity among children and adolescents. However, changes in body size and proportion in this population over time have also influenced BMI. To date, no study of secular changes in childhood obesity has considered the impact of changes in morphological factors. The current study explored the secular changes in BMI and childhood obesity risk among Japanese children from 1950 to 2000 with consideration of changes in body size and the proportions using The Statistical Report of the School Health Survey (SHS). The age of peak velocity (PV) occurred approximately two years earlier in both genders across this period. While the increments in height, sitting height and sub-ischial leg length relative to height levelled off by 1980, weight gain continued in boys. Between 1980 and 2000, the rate of the upper body weight gain in boys and girls were 0.7-1.3 kg/decade and 0.2-1.0 kg/decade, respectively. After considering body proportions, increments in body weight were small. It could be suggested that the increments in weight and BMI across the 50-year period may be due to a combination of changes including the tempo of growth and body size due to lifestyle factors.