Stressful events are inherently emotional. As a result, the ability to regulate emotions is critical in responding effectively to stressors. Differential abilities in the management of stress appear very early in life, compelling a need to better understand factors that may shape the capacity for emotion regulation (ER). Variations in both biologic and behavioural characteristics are thought to influence individual differences in ER development. We sought to determine the differential contributions of temperament and heart rate variability (HRV; an indicator of autonomic nervous system function) to infant resting state emotionality and emotional reactivity in response to a stressor at 6 months of age. Participants included 108 mother-infant dyads. Mothers completed a measure of infant temperament at 6 months postnatal. Mother and infant also participated in a standardized stressor (the Repeated Still Face Paradigm) at that time. Electrocardiographic data were acquired from the infant during a baseline resting state and throughout the stressor. Fast Fourier Transformation was used to analyse the high frequency (HF) domain of HRV, a measure of parasympathetic nervous system activity. Infant ER was measured via standardized coding of emotional distress behaviours from video-records at baseline and throughout the stressor. Severity of mothers' depressive symptoms was included as a covariate in analyses. Results of linear regression indicate that neither temperament nor HRV were associated significantly with an infant's emotional resting state, although a small effect size was found for the relationship between infant negative affectivity and greater emotional distress (β = 0.23, p = 0.08) prior to the stressor. Higher HF-HRV (suggesting parasympathetic dominance) was related to greater emotional distress in response to the stressor (β = 0.34, p = 0.009). This greater emotional reactivity may reflect a more robust capacity to mount an emotional response to the stressor when infants encounter it from a bedrock of parasympathetic activation. Findings may inform eventual markers for assessment of ER in infancy and areas for intervention to enhance infant management of emotions, especially during stressful events.