We compared the motor competence between overweight/obese and eutrophic preschoolers with similar physical activity levels, age, socioeconomic status, maternal education, quality of the home environment and quality of the school environment. We also investigated to what extent excess body fat mass explains gross motor skills in preschoolers. A cross-sectional quantitative and exploratory study was conducted with 48 preschoolers assigned into eutrophic and overweight/obese groups. Overweight/obese preschoolers had worse Locomotor subtest standard scores than the eutrophic ones (p = 0.01), but similar Object Control subtest and Gross Motor Quotient scores (p > 0.05). Excess body fat mass explained 12% of the low Locomotor subtest standard scores in preschoolers (R2 = 0.12; p = 0.007). Excess body fat mass was associated with worse locomotor skills when the model was adjusted for physical activity levels, age, socioeconomic status, maternal education, quality of the home environment and quality of the school environment. Thus, excess body fat mass partly explains lower locomotor skills in preschoolers.