BACKGROUND: Premenstrual syndrome (PMS) is known to be a prevalent health concern affecting a significant number of women globally and yoga is found to be beneficial in such psychosocial disorders. OBJECTIVE: To evaluate the effectiveness of a structured yoga intervention by comparing pre-and post-intervention changes in the severity of PMS symptoms and cardiac autonomic functions in young, healthy female students over the course of three menstrual cycles. METHODS: The present study is a trial conducted in the Department of Physiology, Kasturba Medical College, Manipal which consists of 49 young, healthy female volunteers suffering from moderate PMS. Heart rate variability (HRV) and autonomic functions were assessed via PowerLab, after which yoga training was provided for a 12-week duration in the Division of Yoga, CIMR. HRV and other autonomic function tests were again repeated postintervention. RESULTS: Student's t-test was used to analyze the different parameters, and significant improvements were observed in the time domains of the HRV (i.e. SDNN). There was a significant decrease in the SBP and heart rate. Cardiac autonomic function tests revealed reduced sympathetic drive. CONCLUSION: This study revealed that significant alterations were seen in HRV and autonomic functions during the regular practice of yoga in young healthy females in the premenstrual phase. These findings suggest that regular yoga practice can have beneficial effects on parasympathetic dominance as well as overall well-being by creating a balance in the neuro-endocrinal axis.