Introduction: Overweight and obese children may have lower motor coordination score than normal-weight children. Objective: To compare gross motor coordination between overweight/obese and normal-weight children and investigate the associated factors with the motor coordination scores. Method: This cross-sectional study involved 169 children of both genders, aged 6-9 years. Children with malformations, bone, muscle, and joint or neurological disorders, and BMI z < -2 were excluded. Gross motor coordination was assessed by the “Körperkoordinationstest für Kinder” (KTK). The associated factors with the motor coordination scores were analyzed by linear regression. Results: The mean scores for balancing backwards (84.2 ± 13.2 vs. 91.0 ± 15.0), hopping over on one foot (127.9 ± 10.1 vs. 132.3 ± 12.1), shifting platforms sidewise (123.5 ± 23.4 vs. 129.8 ± 14.9), as well as the overall motor scores (112.5 ± 14.8 vs. 118.8 ± 11.6) were significantly lower (p < 0.05) in overweight/obese children when compared to normal-weight children. The percentage of poor motor scores (< 85) in balancing backwards was higher in overweight/obese children (60.4% vs. 36.4%, p = 0.004) and was similar for jumping sideways (18.8% vs. 9.9%, p = 0.116), as well as for shifting platforms sidewise (6.3% vs. 0.8%, p = 0.070). By multiple linear regression analysis, the variables overweight/obesity and sports practice for less than 2 times/week decreased significantly (p < 0.05) the motor coordination score by -18.7 and -15.6 points, respectively. Conclusion: The overweight/obese children scored lower in the motor coordination tests compared to the normal-weight children. Overweight/obesity and low frequency of physical activity were associated with lower scores of gross motor coordination.