Despite being important in the body’s mechanisms, excessive accumulation of manganese (Mn) can induce severe toxicity in vital organs of the body. Thymoquinone (TQ) is extracted from Nigella sativa seeds which recently gained popularity as dietary supplements and plant-based antioxidants. Vildagliptin (VLD) is a dipeptidyl peptidase IV (DPPIV) inhibitor, approved as antihyperglycemic agents with cardioprotective and renoprotective effects. The present study aimed to investigate the nephrotoxicity of Mn and the potential protective effects of thymoquinone and vildagliptin. Sixty-four adult male albino rats were equally divided into 8 groups: group I (control, received no medication), group II (vehicle, received normal saline), group III (TQ, 50 mg/kg/day), group IV (VLD, 10 mg/kg/day), group V (MnCl2, 50 mg/kg/day), group VI (Mn+TQ), group VII (Mn+VLD), and group VIII (Mn+TQ+VLD). Groups VI, VII, and VIII, received the same previously mentioned doses. All drugs were orally gavaged for 12 weeks. Manganese administration resulted in an elevation in the levels of serum and tissues Mn, blood glucose, serum urea, creatinine, tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6), and reduction in insulin, kidney superoxide dismutase (SOD), glutathione (GSH), and interleukin-10. Histopathological structural renal damage was detected associated with strong positive immunoexpression of caspase-3. On the other hand, individual or combined TQ and VLD administration with Mn significantly decreased the serum and tissue levels of Mn, declined the blood glucose, inflammatory markers, oxidative stress markers, ameliorated the histopathological effects, and down-regulated the immunoexpression of caspase-3. In conclusion, TQ and VLD co-administration elicited protective effects against Mn-induced nephrotoxicity. Keywords Manganese . Oxidative stress . Nigellasativa . Dipeptidyl peptidase inhibitor . Kidney . Cytokines . Apoptosis .