Objective: To investigate longitudinal associations of burnout with heart rate variability (HRV) in patients after their first events of acute coronary syndrome (ACS). Methods: In total, two hundred eight patients participated in this one-year follow-up study. On the day before discharge, their personal burnout level was assessed by the Copenhagen Burnout Inventory. HRV signals were collected at four time points: the day before discharge, one month, six month and one year after discharge. HRV was measured by 24-hour ambulatory electrocardiography and analyzed in time and frequency domains. Generalized estimating equations were applied to analyze the associations of burnout at baseline with longitudinal tracking of HRV during follow-up in format of natural logarithmic transformation. Results: After adjusting for relevant confounding factors, high burnout at baseline was significantly associated with low standard deviation of NN intervals (SDNN), a time domain measure of HRV (p < 0.05). Also, baseline burnout was inversely associated with five frequency domain measures, i.e., high frequency power (HF), low frequency power (LF), very low frequency power (VLF), and ultra low frequency power (ULF), and total power (TP) (all p < 0.05). Conclusion: Personal burnout is longitudinally associated with decreased HRV during one-year period among patients after first ACS.