Nivolumab, a PD-1 inhibitor, enhances anti-tumor immunity but can cause immune-related adverse events (irAEs). Although irAE-colitis usually occurs within 2–3 months of starting nivolumab, we report a rare case that developed 38 months after treatment initiation. A 75-year-old man with metastatic renal cell carcinoma received multiple lines of molecular targeted therapies before starting nivolumab. After progression of bone metastases, nivolumab was reinitiated and maintained a complete response of bilateral iliac bone metastases for three years. He subsequently developed Grade 3 diarrhea. Colonoscopy revealed diffuse inflammation from rectum to sigmoid colon, and pathological examination showed findings consistent with irAE-colitis. Prompt initiation of prednisolone 60 mg/day led to complete symptom resolution within two weeks. This case represents the first reported instance of irAE-colitis occurring after 38 months of nivolumab treatment. It is essential to conduct regular follow-up examinations and actively perform diagnostic tests when symptoms arise, ensuring vigilance for the potential occurrence of delayed-onset irAEs to facilitate appropriate management.