Efforts to increase moderate-to-vigorous physical activity (MVPA) in school-age children are associated with improved health, cognitive, and academic outcomes. However, questions remain about whether similar benefits are observed in early childhood. We hypothesized that motor competence, not MVPA, would be related to improved cognitive and academic skill development in early childhood. For this study, 283 children were recruited from 13 community-based preschools (55% female; M = 4.2 years old, SD = 0.6; 41% non-Hispanic White, 37% non-Hispanic Black; 10% Hispanic, 10% mixed race, 2% Asian, 1% American Indian). Children's physical activity, motor competence, executive function (EF), and math problem-solving skills were measured using the same protocol in three assessments in a single academic year (i.e., fall, winter, spring). Although motor competence was strongly correlated with contemporaneous measures of EF and math problem-solving skills (rs = 0.51-0.63), MVPA was weakly correlated with EF and math problem-solving skills (rs = 0.03-0.18). Mixed linear models demonstrated that improvements in children's motor competence were related to improvements in their EF and math problem-solving skills (ps < 0.001), their improvements in MVPA were not statistically significant related to any of the outcomes. These within-child associations provide a stronger basis of inference by controlling for all time-invariant confounders. The results of this study suggest that efforts to improve motor competence skills in young children may improve EF and math problem-solving skills, though experimental studies are required to rigorously test this idea.