Job boredom refers to an unpleasant state of passiveness at work that has been found to negatively relate to self-reported health. To date, however, the relation between job boredom and physiological indicators of health has not been examined. The present study investigates whether job boredom relates to dysfunction in autonomic nervous system (ANS) activity as indicated by reduced heart rate variability (HRV) during night sleep. The sample of this study consisted of Finnish public sector workers (n = 125). Job boredom was assessed with an electronic questionnaire and HRV with an ambulatory monitoring period of two nights of sleep. The results supported the hypothesis by showing a negative relation between job boredom and HRV, after controlling for demographic and lifestyle factors. The findings extend previous knowledge on the detrimental consequences of job boredom by showing that it is related to dysfunction in ANS activity. Consequently, it is important to acknowledge boredom at work as a threat to occupational health and well-being and pay more attention to how it can be prevented at workplaces.