Difficulties in emotion regulation are associated with development and maintenance of psychopathology. Typically, features of emotion regulation are assessed with self-report questionnaires. Heart rate variability (HRV) is an objective measure proposed as an index of emotional regulation capacity. A limited number of studies have shown that self-reported difficulties in emotion regulation are associated with HRV. However, results from prior studies are inconclusive, and an ecological validation of the association has not yet been tested. Therefore, further exploration of the relation between self-report questionnaires and psychophysiological measures of emotional regulation is needed. The present study investigated the contribution of self-reported emotion regulation difficulties on HRV in a student sample. We expected higher scores on emotion regulation difficulties to be associated with lower vagus-mediated HRV (vmHRV). Sixty-three participants filled out the Difficulties in Emotion Regulation Scale and their resting HRV was assessed. In addition, a subsample of participants provided ambulatory 24-h HRV data, in order to ecologically validate the resting data. Correlation analyses indicated that self-reported difficulties in emotion regulation was negatively associated with vmHRV in both resting HRV and 24-h HRV. Specifically, when exploring the contribution of the different facets of emotion dysregulation, the inability to accept negative emotions showed the strongest association with HRV. The results are discussed and need for future research is described.