Abstract Background: Thymoquinone (TQ) is the most abundant and active ingredient of Nigella sativa (NS) seeds. Its hepatic, renal, and cardiac protective effects have been demonstrated in animal models. Streptozotocin (STZ) is an antibiotic that is widely used experimentally as an agent capable of inducing insulin-dependent diabetes mellitus (IDDM), also known as type I diabetes mellitus (T1DM). Objectives: This study was carried out in an attempt to highlight the possible beneficial effects of TQ in STZ-induced diabetes in rats and to determine the predictive value of mesenchymal and epithelial markers in the response of diabetic nephropathy to TQ. Materials and Methods: Sixty adult male albino rats were divided in 3 groups: control, diabetic untreated, and diabetic treated with TQ. Results: Diabetic rats exhibited morphological changes in both renal glomeruli and tubules with immunohistochemical expression of the mesenchymal markers Fsp1, desmin, and MMP-17 and disappearance of the epithelial marker ZO-1 largely in the glomeruli of diabetic kidneys. Treatment with TQ significantly attenuated renal morphological and immunohistochemical changes in STZ-induced diabetic rats. Conclusions: Thymoquinone has protective effects on experimental diabetic nephropathy. Both mesenchymal and epithelial markers serve as excellent predictors of early kidney damage and indicators of TQ responsiveness in STZ-induced diabetic nephropathy.