Globally, more than half of school-aged children do not engage in the recommended 60 minutes of daily moderate to vigorous physical activity (MVPA). Given that developing sufficient fundamental motor skills (FMS) competence during early elementary school years is important for a child’s physical and cognitive development, the purpose of this study was to examine the effects of an 8-week FMS-based afterschool program on physical and cognitive health outcomes among elementary children. Participants were 31 K–2 students (19 girls, 12 boys; Mage = 6.65 ± 0.98) from three public elementary schools in the southwestern United States who were assigned to the intervention group (FMS-based afterschool program; n = 20) or the control group (traditional afterschool program; n = 11). A 2 × 2 repeated measures MANOVA showed significant changes in FMS competence and MVPA between the intervention and the control group over time. However, no significant changes were found in cognitive functioning. The 8-week FMS-based afterschool program showed significant improvements in FMS competence and MVPA, compared to a traditional afterschool program. This finding suggests that structured FMS-focused strategies (e.g., fun games and goal setting) can be a critical component when implementing a physical activity program to enhance children’s motor skills and physical activity behavior.