Background and Study Aim. Fundamental motor skills in children serve as the basis for constructing more complex movement patterns. Therefore, the quality of mastering these skills, relative to children's age, largely determines success. These skills are influenced by both gender and weight status. This study aimed to analyze gender differences and the relationship between BMI and motor competence in school-aged children. Materials and Methods. A cross-sectional study was conducted among 260 children (130 boys and 130 girls) aged 9–13 years from three schools in Mumbai, India. Motor competence was evaluated using the Basic Motor Skills Assessment Scale. The scale assessed locomotor skills, object control, and turning and rolling. Anthropometric data were collected to calculate BMI, categorized as normal, overweight (≥85th percentile), and obese (≥97th percentile). Extracurricular physical activity habits were assessed through a structured questionnaire. Statistical analyses included chi-square tests, t-tests, and one-way ANOVA with Scheffé post hoc comparisons (p < 0.05). Results. Among the sample, 19.2% were overweight and 11.6% were obese. Boys showed significantly greater engagement in extracurricular physical activity than girls (t = 3.214, p = 0.002). Boys preferred team-based sports, while girls favored individual activities. Significant intragender differences in locomotor and turning/rolling skills were found among boys. Normal-weight boys outperformed both overweight (p = 0.002) and obese peers (p = 0.001, 0.019, respectively). Obese boys also showed significantly lower turning and rolling competence than overweight boys (p = 0.011). In object control, normal-weight boys and girls both demonstrated superior performance compared to obese counterparts (p = 0.018 for boys; p = 0.010 for girls). Among girls, no significant differences were observed in locomotor or turning/rolling skills across BMI categories. Conclusions. Gender and BMI significantly impact motor competence in children. Interventions should consider these factors to support inclusive physical development and target the needs of overweight and obese children.