Background: Although many studies have been conducted to compare the effect of adherence to a low-carbohydrate diet (LCD) with a low-fat diet (LFD) on anthropometric indices and body fat percentage, there is still no definite conclusion in this regard. Therefore, the present study aims to summarize results of studies comparing a LFD and a LCD on weight loss. Methods: A systematic search of databases including PubMed, Scopus, and Cochran Library was performed up to November 2020. All randomized controlled trials (RCTs) comparing the effect of adherence to a LCD with a LFD on anthropometric indices and body fat percentage were included. Search results were limited to English-language publications. Sixty-three RCTs, including 7660 participants, were selected for the present study. Results: Pooled analysis indicated that adherence to LCD was significantly associated with a greater reduction in BMI (SMD = - 0.07, 95% CI: -0.14,-0.001; P = 0.04), weight (kg) (SMD = - 0.22, 95% CI: - 0.31, - 0.12; P ≤ 0.001), and percentage of body fat mass (SMD = - 0.28, 95% CI: -0.48, - 0.08; P = 0.006) compared to LFD. However, no significant difference in changes of kilogram of body fat mass and waist circumference was observed between the two diet programs. Conclusion: Overall, adhering to LCD was more effective than LFD in losing weight and body fat percentage.