A 50-year-old man was diagnosed with right staghorn calculus. Urine cytology showed atypical cells, and he was followed for suspicion of urothelial carcinoma. However, there was no evidence of tumor six months later, and percutaneous nephrolithotripsy (PNL) was performed for right staghorn calculus. Eight months later, renal pelvic squamous cell carcinoma extending to the abdominal wall through the nephrostomy tract was identified. After neoadjuvant chemotherapy, radical nephroureterectomy and enbloc resection of the nephrostomy tract tumor was performed. The renal pelvic squamous cell carcinoma did not recur. However he died of small cell lung cancer 3 years postoperatively. Planning of treatment strategy was difficult in the present case. Even though PNL was performed after sufficient follow up and examination, renal pelvic cancer could not be diagnosed and extended to the PNL tract. Fortunately, radical en-bloc resection was possible. We herein, report a case of renal pelvic squamous cell carcinoma after PNL.