Urolithiasis is a well-known and common late complication in patients with urinary diversion. Patients without urinary diversion lead to symptoms such as hematuria and ureteral colic, whereas stones in patients with urinary diversion tend to be asymptomatic and are often diagnosed incidentally during staging examinations of oncologic diseases. We report the case of a 64-year-old male patient with a lower pole kidney stone and a stone in the ileal ureter substitution. He presented with diffuse abdominal and left-sided flank pain. CT revealed the diagnosis of urolithiasis in the ileal ureter substitution and the lower pole of the left kidney. We performed a combined retrograde, flexible ureteroscopy and a mini percutaneous nephrolithotomy (combined intrarenal surgery) without any complications and no residual stone fragments postoperatively. This case presentation demonstrates that in patients with urinary tract diversion, urolithiasis can still cause problems.