In recent years, studies have focused on the factors affecting physical fitness in children; however, the relationship between physical fitness and social-emotional skills has not been explored. This study aimed to clarify the relationship between the physical fitness of children and their social-emotional skills. The subjects were 822 children in grades 3-6 of elementary school. We administered a questionnaire survey utilizing the New Physical Fitness Test28) and a rating scale to evaluate the social-emotional skills of elementary school children50). We calculated and analyzed partial correlation coefficients considering age to assess the relationship between the overall physical fitness score, individual physical fitness test results, and the total social and emotional skills score along with its subscale scores. A weak correlation was observed between the total physical fitness score and the total social-emotional skill score in boys and girls (boys: r = 0.285, p < .05, girls: r = 0.238, p < .05). A significantly low relationship was identified between total physical fitness score and the scores of the subitems in social and emotional skills including patience, sociability, and self-esteem for boys and girls. Upon analysis of each grade, a significant correlation was observed between the total physical fitness score, the total social-emotional skills score, and the social-emotional skills subitem score in boys and girls sixth-grade students. In conclusion, we observed a relationship between physical fitness and social-emotional skills in elementary school children in the middle and upper grades. Moreover, the study found that the correlation varied depending on the specific social-emotional skills, and it was more pronounced among sixth graders than students in other grades.