While there is wide consensus regarding the importance of early intervention, health is rarely considered within priorities. Twenty-five children on the autism spectrum (Mage = 4.67, SD = 0.82) participated in a 12-week physical activity intervention. Primary objective was to examine impact of a physical activity intervention on physical activity, fitness and motor competence. Secondary objective was to examine associations between motor behavior and ASD symptoms. Ball skills (p < .001) and isometric push-up performance (p = .02) improved. Autism symptoms were associated with motor skills (r > − .49, p < .05). Study outcomes provide new knowledge regarding design, delivery, and measures for early interventions targeting health disparities in young children on the autism spectrum.