While there is wide consensus regarding the importance of early intervention, health is rarely considered within priorities. Twenty-five children on the autism spectrum ( M age = 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. Supplementary Information The online version contains supplementary material available at 10.1007/s10803-021-04871-7.