This study aimed to explore changes in heart rate variability (HRV), a proxy for parasympathetic activity characterizing emotion regulation processes before, during and after negative emotional induction in patients suffering from restrictive type anorexia nervosa (AN-RT). We compared two methods of HRV analysis, the Fast Fourier Transform high frequency (FFT-HF) and a specific HRV high frequency analysis technique, namely, the wavelet transform HRV (WT-HRV). A sample of 16 inpatients with AN-RT was compared to 24 control participants. Heart rate (HR) was continuously recorded for 5 min before the beginning of the video until 5 min after the video. The participants answered questionnaires concerning their eating behaviors, mood disorders and difficulties in emotion regulation. During the entire procedure, the FFT-HF in patients was lower than that in controls. Using the WT-HRV, the patients did not differ from the controls at baseline, and only the controls showed a decrease during emotional induction. After the video, the WT-HRV in patients began to decrease during the first 2 min of emotional recovery although the WT-HRV in controls was already increased. These results highlighted the disturbances in the physiological dynamics of emotion regulation processes in patients with AN-RT.