Type 2 diabetes mellitus (T2DM) is a progressive metabolic disorder mainly caused by overweight and obesity that accumulates pro-inflammatory factors in adipose tissue. Studies have confirmed the efficacy of exercise and vitamin D supplementation in preventing, controlling, and treating diabetes. While, reduced physical activity and vitamin D deficiency are related to increased adiposity, blood glucose level, insulin concentration, and insulin resistance. This study purposed to investigate the effect of 8-week aerobic training with vitamin D supplementation on the expression of AMPK, PGC-1α, and UCP-1 genes expression in the visceral adipose tissue of obese rats with T2DM. In this experimental study, fifty male Wistar rats were divided into 5 groups (n = 10): aerobic training and vitamin D supplementation (AT + Vit D), aerobic training (5 days/week for 8 weeks; AT), vitamin D supplementation (Vit D), diabetic control (C) and NC (Non-Diabetic Control). AT + Vit D and AT groups practiced an 8-week aerobic training, 5 days a week. Vit D and AT + Vit D groups receive 5000 IU of vitamin D by injection once a week while AT and C received sesame oil. After blood sampling, visceral fat was taken to measure AMPK, PGC-1α, and UCP1 gene expression. Data were statistically analyzed by One-way ANOVA and paired samplet-test at a significance level of p < 0.05. Based on our results BW, BMI, WC, visceral fat, insulin, glucose, and HOMA-IR were significantly lower in the AT + Vit D, AT, and Vit D groups compared with the C group (p < 0.01). Furthermore, AT + Vit D, AT, and Vit D upregulated AMPK, PGC-1α, and UCP1 gene expression compared to the C. Based on the results compared to AT and Vit D, AT + Vit D significantly upregulated AMPK (p = 0.004; p = 0.001), PGC-1α (p = 0.010; p = 0.001), and UCP1 (p = 0.032; p = 0.001) gene expression, respectively. Also, AT induced more significant upregulations in the AMPK (p = 0.001), PGC-1α (p = 0.001), and UCP1 gene expression (p = 0.001) than Vit D. Vitamin D supplementation enhanced the beneficial effects of aerobic training on BW, BMI, WC, visceral fat, insulin, glucose, and HOMA-IR in diabetic rats. We also observed that separate AT or Vit D upregulated the gene expression of AMPK, PGC-1α, and UCP1 however, combined AT + Vit D upregulated AMPK, PGC-1α, and UCP1 more significantly. These results suggested that combining aerobic training and vitamin D supplementation exerted incremental effects on the gene expressions related to adipose tissue in animal models of diabetes.