A 73-year-old woman was referred to our department with a complaint of asymptomatic gross hematuria. Dynamic computed tomography revealed a complicated (Bosniak type IIF) cyst in the upper pole of her right kidney, which was diagnosed as a calyceal diverticulum. The diagnosis was confirmed by ureteroscopy. The diverticulum was filled with a soft protein matrix that was difficult to completely remove from the inner surface of the calyceal diverticulum. Endoscopy combined with intrarenal surgery (ECIRS) was performed to completely remove the matrix. Percutaneous nephroscopy further revealed papillary lesions on the surface of the diverticulum, confirmed as squamous cell carcinoma on pathological assessment. A laparoscopic right radical nephroureterectomy was performed, with curative intent. Pathological assessment confirmed a high-grade squamous cell carcinoma with renal parenchymal invasion (pT3). Although carcinomas in a calyceal diverticulum are highly uncommon, when present, these tend to be high-grade neoplasms that deeply invade the parenchymal wall. As the effective management of these lesions is difficult, early-stage diagnosis is required for curative treatment. We report the case of squamous cell carcinoma in a calyceal diverticulum that was difficult to diagnose on preoperative computed tomography, urinal cytology examination, and ureteroscopy but was found during ECIRS.