Individual differences in heart rate variability (HRV) at rest are thought to represent an individual\'s capacity for self-regulation, but it remains unclear whether HRV predicts control over unwanted thoughts. The current study used a thought suppression paradigm in which participants recorded occurrences of a personally relevant intrusive thought over three monitoring periods. Among those instructed to suppress, higher levels of HRV were associated with greater declines in intrusions across the monitoring periods; no such relationship was found among those assigned to a control condition. Resting HRV also interacted with spontaneous thought suppression effort to predict intrusive thought frequency. In both cases, these HRV-related differences in thought suppression success predicted the generalized distress symptoms common to depression and anxiety. These findings enhance understanding of the relationships between HRV and cognitive control and highlight how individual differences in self-regulatory capacity impact thought suppression success and emotion regulation.