Background: Meditation refers to a group of practices commonly proposed to treat stress-related conditions and improve overall wellness. In particular, meditation might exert beneficial actions on heart rate variability (HRV) by acting on autonomic tone with an increase in the vagal activity. The effects of heartfulness meditation (HM) on HRV remain poorly defined. Methods: We investigated the effects of HM on HRV in a group of 26 healthy subjects. Subjects were regularly practicing this form of meditation on a daily basis. We assessed the HRV and residual HRV (rHRV) at rest and during meditation. We also used as control a period of respiratory rhythm imposed by an auditory signal, with the imposed breathing rhythm being identical to the spontaneous rhythm recorded during meditation. Results: During deep meditation period, the standard deviation of RR intervals (SDRR), coefficient of variation of RR intervals (CVRR), and total power (TP) were decreased while the low-frequency power (LFP), normalized LFP (nLFP), and normalized residual LFP (nrLFP) were increased as compared with those at rest, suggesting that the global vagal modulation was suppressed while the baroreflex was increased during deep medication. At the end of meditation, the LFP, residual LFP (rLFP), nLFP, nrLFP, low-/high-frequency power ratio (LHR), and residual LHR (rLHR) were increased while the residual very low-frequency power (rVLFP), normalized high-frequency power (nHFP), and normalized residual HFP (nrHFP) were decreased, as compared with those during paced breathing, suggesting that the vagal modulation was decreased while the sympathetic modulation was increased by deep meditation. During paced breathing period, the SDRR, CVRR, TP, LFP, rLFP, nLFP, nrLFP, LHR, and rLHR were decreased while nHFP and nrHFP were increased as compared with at rest, suggesting that paced breathing could suppress the sympathetic modulation and enhance the vagal modulation. Conclusion: HM can induce a suppression of global vagal modulation and increased the sympathetic modulation and baroreflex. In addition, paced breathing can suppress the sympathetic modulation and enhance the vagal modulation. Unlike studies using other types of meditation, we did not identify evidence of increased vagal tone during HM.