Background: Physical literacy-focused afterschool activity programs (ASAPs) can be an effective strategy to improve children's health-related parameters. We sought to compare physical activity, body composition, aerobic capacity, and fundamental movement skills between physical literacy-focused ASAP and a standard recreational ASAP. Method: A pre-post (6 months) comparison study was conducted in 5- to 12-year-old children in a physical literacy-focused ASAP (physical literacy group, n = 14) and children attending a standard recreational ASAP (comparison group, n = 15). Physical activity guideline adherence was assessed using accelerometry, body composition was analyzed using bioelectrical impedance, aerobic capacity was estimated using the Progressive Aerobic Cardiovascular Endurance Run test, and fundamental movement skills were evaluated using the Test of Gross Motor Development--2. Results: There were no significant differences between groups at baseline. After 6 months, the physical literacy group exhibited a significant improvement in their total raw score for the Test of Gross Motor Development--2 (p = 0.016), which was likely due to improvements in object control skills (p = 0.024). The comparison group significantly increased body mass index (p = 0.001) and body fat (p = 0.009) over time. No significant between-group differences were found; however, there was a trend for improved aerobic capacity in the physical literacy group (d = 0.58). Conclusions: Engagement in the physical literacy-focused ASAP contributed to an attenuated increase in adiposity and an improvement in object control skills.