The current study aimed to investigate the molecular mechanisms of metformin and vitamin D3-induced nephroprotection in a MetS rat model, evaluating the capacity of vitamin D3 to potentiate metformin action. MetS was induced by 10% fructose in drinking water and 3% salt of the diet. After 6 weeks, serum lipid profile and uric acid were measured, an OGTT was performed and kidney function was investigated. MetS rats with significant weight gain, dyslipidemia, hyperuricemia and dysglycemia were treated orally with metformin (200 mg/kg), vitamin D3 (10 µg/kg) or both daily for 6 weeks. At the end of the study period, anthropometrical parameters were recorded, OGTT was reperformed, urine and blood samples were collected and tissue samples were harvested at sacrifice. MetS rats showed dramatically declined renal function, enhanced intrarenal oxidative stress and inflammation and extravagant renal histopathological damages with interstitial fibrosis. Metformin and vitamin D3 significantly reversed all the aforementioned deleterious effects in MetS rats. The study has verified the nephroprotective effects of metformin and vitamin D3 in MetS, accentuating the critical role of AMPK/SIRT1 activation and DPP-4 inhibition. Given the synergistic effects of the combination, vitamin D3 is worth being investigated as an additional therapeutic agent for preventing MetS-induced nephropathy.