The relationship between body fat growth and physical fitness and motor ability development in school age children is not well understood. We determined the similarities and differences in body fat growth and physical fitness and motor ability development curves by applying cross correlation functions, and attempted to show the structure of growth and development between these attributes. The subjects were 647 boys aged 7 to 15 years. The measurements were height, weight, body mass index and body fat percentage as physical characters; and 20-m sprint, Pro Agility test, side steps, standing long jump, vertical jump, and rebound jump (RJ) index as physical fitness and motor ability. The wavelet interpolation method was applied to growth and distance values for physique, body fat and physical fitness and motor ability, and growth and development curves were derived. Cross correlation functions were then applied to the respective pairs of the compared velocity curves. There were large changes in the behavior of the growth velocity curve around the take off age for height, and so the relationship between body fat percentage and physical fitness and motor ability was investigated using the respective cross correlation functions around the take off age. Before the take off age, positive correlations were seen between body fat percentage and physical fitness and physical fitness and motor ability except for the RJ index. After the take off age, in contrast, there were negative correlations between body fat percentage and physical fitness and motor ability except for the RJ index. These results show the new finding that after the take off age in boys, there are contrary similarity between body fat and speed, agility, and instantaneous force.