In addition to social communication deficits, restricted repetitive behaviors (RRBs) are a key diagnostic feature of autism spectrum disorder (ASD). Dysfunction of the autonomic nervous system (ANS) in ASD has been posited as a mechanism of RRBs; however, most studies investigating ANS activity in ASD have focused on its relation to social functioning. This study used respiratory sinus arrhythmia (RSA) patterns to measure ANS functioning and analyze its relation to RRBs in children with and without an ASD diagnosis. Baseline RSA and RSA reactivity predicted RRB severity and exploratory analyses revealed these measures may be associated with RRB subgroups. These results are discussed in regards to the behavioral literature on RRBs and the benefits of finding biomarkers for these behaviors.