The role of non-alcoholic fatty liver disease (NAFLD) as a potential independent cardiovascular disease (CVD) risk factor has recently gained considerable attention because CVD is the common cause of death in NAFLD patients. We aimed to estimate the effects of vitamin D supplementation alone or in combination with calcium on atherogenic indices, liver function tests, and grade of disease in patients with NAFLD. One-hundred twenty NAFLD patients were randomized in a double-blind, placebo-controlled clinical trial as follows: D (1000 IU vitamin D), CaD (500 mg as calcium carbonate plus 1000 IU vitamin D) or P (placebo), once daily with meals over 12 weeks. Adjusted for all the baseline measures, reduction in serum ALT, AST, LDL-C/HDL-C, TC/HDL-C, and non-HDL-C were significantly higher in the CaD compared with the P group (p < 0. 001, p = 0. 03, p < 0. 001, p < 0. 001, p < 0. 001 and p < 0. 001, respectively). Also, mean difference of serum ALT, LDL-C/HDL-C, TC/HDL-C, and TG/HDL-C were significantly higher in the CaD than D group (p < 0. 001, p = 0. 006, p < 0. 001 and p = 0. 03, respectively). Serum non-HDL-C was marginally decreased in the CaD compared with the D group (p = 0. 06). With considering the BMI changes as covariate, reduction in the grade of fatty liver was significantly higher in the CaD and D groups than the P (p < 0. 001). The present study suggests that supplemental calcium combined with vitamin D, but not vitamin D alone, may reduce serum atherogenic indices, liver function tests, and grade of disease in patients with NAFLD.