Temporomandibular disorders (TMDs) are the most common cause of non-dental chronic pain in the orofacial region and can chronically increase the activity of the allostatic systems. The allostatic overload related to these conditions causes an autonomic dysregulation, reflected by a reduction in heart rate variability (HRV). Nevertheless, chronic pain in these patients could cause more severe health consequences, such as those related to cognitive functioning. Deficits in executive control have been associated with allostatic overload and could negatively affect pain management strategies. This study aimed to investigate the effects of chronic pain on HRV and both motor and cognitive inhibition (assessed with the Go/No-Go and Stroop tasks, respectively) in a sample of 14 patients with TMD and 15 healthy controls. Consistent with our hypothesis and the previous literature, the group with TMD had a lower resting HRV, but no differences were found between the groups in inhibition. Furthermore, the results showed that the effects of HRV on cognitive inhibition can be mediated by pain intensity. Finally, a correlation between age and HRV emerged in patients with TMD but not in healthy controls.