The objective of this study was to evaluate the effect of vitamin D3 on total homocysteine (tHcy) and C-reactive protein (CRP) levels and liver and kidney function tests in overweight women with vitamin D deficiency. Therefore, a randomized double-blind placebo controlled clinical trial was conducted on one hundred eligible women. Subjects were randomly divided into two groups: the placebo (n = 50) and the vitamin D (n = 50) which received 50,000 IU vitamin D3 per week for 2 months. The participants’ 25- hydroxyvitamin D (25 (OH)D), tHcy, CRP, aspartate and alanine aminotransferases (AST, ALT), urea, creatinine and estimated glomerular filtration rate (eGFR) were measured and compared before and after treatment. Results showed that the tHcy, CRP, AST, ALT, and eGFR levels after the second month of vitamin D3 intervention were significantly (p < 0.001) decreased and the 25(OH)D, urea, and creatinine levels were significantly (p < 0.001) increased in the treatment group. In the placebo group, no significant changes were identified throughout the follow up period. In conclusion, vitamin D3 intervention with a treatment dose of 50,000 IU per week for at least 2 months may help in lowering homocysteine and CRP levels and may improve liver function tests, which in turn might help in minimizing the risk of CVD and liver diseases among overweight women but negatively affect kidney function.