It has recently been reported that black rice (BR) extract has anti-obesity, anti-diabetic, and anti-osteoporosis effects. It has been shown to reduce obese-related kidney dysfunction in animal models. This study aimed to investigate the effect of resistant starch from BR (RS) on renal inflammation, oxidative stress, and apoptosis in obese insulin resistant rats. Male Wistar rats were divided into six groups: normal diet (ND), ND treated with 150 mg of RS (NDRS150), high-fat (HF) diet, HF treated with 100 and 150 mg of RS (HFRS100), (HFRS150), and HF treated with metformin as a positive control. Insulin resistance was shown in the HF rats by glucose intolerance, increased insulin, total area under the curve of glucose and homeostasis model assessment of insulin resistance and dyslipidemia. The resulting metabolic disturbance in the HF rats caused renal inflammation, fibrosis and apoptosis progressing to kidney injury and dysfunction. Prebiotic RS including anthocyanin from BR at doses of 100 and 150 mg ameliorated insulin resistance, dyslipidemia and liver injury. Treatment with RS reduced TGF-β fibrotic and apoptotic pathways by inhibition of NF-κB and inflammatory cytokines which potentially restore kidney damage and dysfunction. In conclusion, prebiotic RS from BR ameliorated obesity induced renal injury and dysfunction by attenuating inflammatory, fibrotic, and apoptotic pathways in insulin resistant rats induced by HF.