Previous studies reported inconsistent findings regarding the effects of magnesium supplementation on obesity measures. This study was done to quantify the effect of magnesium supplementation on body weight, Body Mass Index (BMI), Waist Circumference (WC), Body Fat (BF) percentage and Waist to Hip Ratio (WHR). Four online databases (Scopus, PubMed, Google Scholar and Cochrane library) were searched until March 2020 using relevant keywords. Random-effects model was used to pool effect sizes; Cochran's Q-test and I2 index assessed heterogeneity. Sensitivity analysis and Egger test were used to check the robustness of findings and the possibility of publication bias, respectively. Thirty-two RCTs including different dosage of magnesium (48-450 mg/d), and duration (6-24 weeks) were entered to this study. Magnesium supplementation resulted in a great reduction in BMI [Weighted Mean Difference (WMD): -0.21 kg/m, 95% CI: -0.41, -0.001,  = 0.048,  = 89.5%,  = 22], which was mainly driven by the effect among those with magnesium deficiency, insulin resistance related disorders, and obesity at baseline. No significant change was observed in bodyweight, WC, BF percentage and WHR as compared to controls. However, the change in body weight, and WC was significant in subgroups of participants with insulin resistance related disorders, hypertension, obesity, magnesium deficiency at baseline, and females. We found a significant reduction in BMI following magnesium supplementation. The change in body weight and WC were evident in certain subgroups.