Purpose: This study sought to determine whether respiratory sinus arrhythmia (RSA) and executive functions are associated with stuttered speech disfluencies of young children who do (CWS) and do not stutter (CWNS). Method: Thirty-six young CWS and 36 CWNS were exposed to neutral, negative, and positive emotion-inducing video clips, followed by their participation in speaking tasks. During the neutral video, we measured baseline RSA, a physiological index of emotion regulation, and during video viewing and speaking, we measured RSA change from baseline, a physiological index of regulatory responses during challenge. Participants' caregivers completed the Children's Behavior Questionnaire from which a composite score of the inhibitory control and attentional focusing subscales served to index executive functioning. Results: For both CWS and CWNS, greater decrease of RSA during both video viewing and speaking was associated with more stuttering. During speaking, CWS with lower executive functioning exhibited a negative association between RSA change and stuttering; conversely, CWNS with higher executive functioning exhibited a negative association between RSA change and stuttering. Conclusion: Findings suggest that decreased RSA during video viewing and speaking is associated with increased stuttering and young CWS differ from CWNS in terms of how their executive functions moderate the relation between RSA change and stuttered disfluencies.