Background: Body composition and motor skill development are important for the engagement in physical activity and healthy development of children. This study examined the associations between body composition and motor skill development in 3- to 5-year-old children. Methods: Data from preschool-aged children (N = 342, 51% males) who participated in the 2012 National Youth Fitness Survey were analyzed. Skinfold measurements (subscapular, calf, and triceps) were taken and percent body fat (%BF) was calculated using sex-specific equations. Lean muscle mass and fat mass were also calculated. Motor skill development was determined by the Test of Gross Motor Development-2nd Edition. Regression analyses were performed to determine the associations among %BF and locomotor skills, object control skills, and overall gross motor quotient (GMQ), controlling for sex, race, and poverty index ratio. Results: Most children were classified as with underweight/healthy weight (69%) and 31% were either with overweight or obesity. Average %BF was 17.02% ± 0.27%. The standard scores for locomotor skills, object control skills, and GMQ were 9.99 ± 0.16, 8.52 ± 0.14, and 95.57 ± 0.68, respectively. These scores were considered average. Regression analyses indicated that neither the %BF nor sum of skinfolds was associated with locomotor skills (β = -0.07 ± 0.05, p = 0.63; β = -0.03 ± 0.03, p = 0.22), object control skills (β = 0.03 ± 0.04, p = 0.55; β = 0.00 ± 0.02, p = 0.87), or GMQ (β = -0.13 ± 0.28, p = 0.63; β = -0.09 ± 0.14, p = 0.52). Furthermore, neither lean muscle mass nor fat mass was related with any motor skill measure (p > 0.05). Conclusions: Using different measures of body composition may provide additional insight into associations between obesity and motor skill development in preschool-aged children. Given the inconsistent findings in the literature, additional research is needed to elucidate these associations.