Background: Obesity in children is a serious public health problem, affecting their physical health and quality of life. Fundamental movement skills (FMS) have been suggested to play an important role in reducing the risk of obesity in primary school children and improving their health-related quality of life (HRQoL). Objectives: This study aims to investigate the relationship between body mass index (BMI), FMS, and HRQoL in primary school children. Methods: 193 primary school children (81 boys, 112 girls) aged 6 to 8 years were included in this cross-sectional study. Weight and height, FMS, and HRQoL were measured using BMI percentiles, the Test of Gross Motor Development, Second Edition (TGMD-2) including the object control, locomotor subtests and the total gross motor quotient, and the Pediatric Quality of Life Inventory (PedsQLTM) respectively. Results: There was a negative significant correlation between BMI and gross motor quotient, and between BMI and the locomotor subscale of the TGMD. There was also a negative significant correlation between BMI and the PedsQL scale. There was a positive significant correlation between TGMD and PedsQoL scales. According to linear regression analysis, BMI significantly predicted TGMD gross motor quotient and PedsQL total score. In addition, the TGMD gross motor quotient significantly predicted the total PedsQL score. Conclusion: Mastery of FMS might be an important factor in avoiding obesity and improving HRQoL in primary school children.