This study aimed to investigate the relationship of body mass index (BMI) with muscle and cardiorespiratory fitness in children living within rural areas (regional unit of West Attica) in Greece. Participants included 399 students (187 boys, 212 girls), ages 8–12 years old, and were evaluated in physical performance tests. The point prevalence of overweight and obesity was 21.39% and 26.20% in boys, and 19.90% and 23.79% in girls. Significant differences were observed in all physical performance tests (handgrip, long jump, shuttle run, trunk flexors, and extensors endurance) between normal weight and obese participants. BMI was positively correlated with handgrip (r = 0.442−0.462, p < 0.001). There was a negative association with long jump (r = −0.206, p < 0.001), 20 m shuttle run (r = −0.394, p < 0.001), trunk flexors (r = −0.403, p < 0.001) and trunk extensors endurance (r = −0.280, p < 0.001). The regression analysis showed that 20–30% of the overall variation for physical performance assessments could be accounted for by BMI, age, and sex. With the exception of the long jump and the endurance of the trunk extensors, BMI alone may explain more than 10% of the outcome of most tests. This study highlights the determinant of BMI on muscle and cardiorespiratory fitness. The management of obesity should begin early in childhood to prevent adult chronic cardiovascular and metabolic diseases.