Abstract. Background and Objective: The aim of present study was to compare, and determine, the effects of a modified alternate-day fasting diet vs. calorie restriction on inflammatory indices and coagulation factors. Methods: This was a randomized clinical trial consisting of 80 metabolic syndrome patients, who were enrolled and randomly dichotomized into a modified alternate-day fasting diet or calorie restriction group for 4 months. We measured weight, body mass index (BMI), waist circumstance (WC), waist-hip-ratio (WHR) and fat mass as primary outcomes and assessed high sensitivity C-reactive protein (hs-CRP), interleukin 6 (IL-6), tumor necrosis factor alpha (TNF-α) and coagulation factors levels as secondary outcomes before and after intervention. Results: Compared to the calorie restriction diet, following a modified alternate-day fasting diet led to a greater reduction in body weight (kg) (–6.43 ± 4.34 vs –4.11 ± 4.27; P = 0.02), BMI (kg/m2) (–3.19 ± 2.90 vs –1.43 ± 2.72; P = 0.01), fat mass (kg) (–4.88 ± 2.09 vs –3.72 ± 2.43; P = 0.03), WC (cm) (–5.57 ± 5.64 vs –2.32 ± 5.95; P = 0.01) and WHR (–0.05 ± 0.06 vs –0.02 ± 0.07; P = 0.04). Furthermore, a greater change was found in hs-CRP levels (mg/L) (–2.06 ± 1.18 vs –0.97 ± 0.82; P = 0.03), prothrombin time (s) (1.41 ± 2.34 vs –0.41 ± 2.17; P < 0.001), activated partial thromboplastin time (s) (0.26 ± 3.70 vs –1.78 ± 3.56; P = 0.04) in modified alternate-day fasting diet when compared to calorie restriction diet. However, there was no difference in TNF-α or IL-6 and fibrinogen between groups (P > 0.05). Conclusions: These findings suggest that a modified alternate-day fasting diet can be a beneficial alternative for the management of body weight, fat mass and WC as well as hs-CRP and coagulation factors levels among metabolic syndrome patients.