Autonomic nervous system (ANS) activity during sensory stimulation was measured in 59 children with autism spectrum disorder (ASD) ages 6–9 in comparison to 30 typically developing controls. Multivariate comparisons revealed significant differences between groups in the respiratory sinus arrhythmia (parasympathetic measure) vector of means across sensory stimuli (p = 0.02) and in change from domain to domain (p = 0.01). Sympathetic activity, measured by pre-ejection period, did not differ significantly between groups, although it was higher in ASD participants. Findings suggest that participants with ASD demonstrated a different pattern of parasympathetic activity during sensory stimulation. Findings are discussed in relation to the biological mechanisms of sensory processing in autism, insight into the autism phenotype, and the utility of ANS activity as an outcomes marker.