Background Sub clinical cardiac autonomic imbalance is associated with depression. Clinical improvement produced by antidepressant therapy might alter this autonomic balance. Objectives To investigate the effect of repetitive transcranial magnetic stimulation (rTMS) therapy on autonomic functions measured by heart rate variability (HRV) in depression patients and compare it with selective serotonin re-up-take inhibitors (SSRI) therapy. Methods Consecutive drug-naïve patients of major depression based on DSM-IV-TR were recruited in this study ( n = 67). Basal Hamilton depression-rating scale (HDRS) and measures of cardiac autonomic function were recorded and compared with those after two weeks of therapy with rTMS ( n = 27) and one month after SSRI therapy ( n = 25). Results Both therapies produced comparable and significant reduction in HDRS scores. HRV measures indicated that rTMS produced significantly greater reduction in the sympathetic: parasympathetic ratio suggesting improvement in sympathovagal balance. Conventional cardiac autonomic function tests did not differentiate the two therapy effects. Conclusions rTMS not only produced antidepressant effects but also ‘‘corrected’’ the autonomic imbalance. SSRI was systemically administered and hence by direct cardiac effect, may have masked cardiac effects that would have occurred by the improvement in depression. Alternatively, the neurophysiological ‘‘correction’’ with drug therapy may have longer latency, just as with the therapeutic effects.