Background: Caring for a loved one can be rewarding but is also associated with substantial caregiver burden, developing mental outcomes and affecting happiness. The aim of this study was to determine the effects of a four-week, 16-h presential meditation program on physiological and psychological parameters and vagal nerve activity in high-burden caregivers, as compared to a control group. Methods: A non-randomized repeated-measures controlled clinical trial was conducted. Results: According to the ANCOVA results, the global happiness score (F = 297.42, p < 0.001) and the scores for all subscales were significantly higher in the experimental group than in the control group at 5 weeks. Anxiety levels were also significantly reduced in the experimental group (F = 24.92, p < 0.001), systolic (F = 16.23, p < 0.001) and diastolic blood (F = 34.39, p < 0.001) pressures, and the resting heart rate (F = 17.90, p < 0.05). HRV results revealed significant between-group differences in the HRV Index (F = 8.40, p < 0.05), SDNN (F = 13.59, p < 0.05), and RMSSD (F = 10.72, p < 0.05) in the time domain, and HF (F = 4.82 p < 0.05)) in the frequency domain, which were all improved in the experimental group after the meditation program. Conclusions: Meditation can be a useful therapy to enhance the mental health and autonomic nervous system balance of informal caregivers, improving symptoms of physical and mental overload.