Spina bifida is a congenital condition that often leads to significant urological complications, including an increased risk of kidney and bladder stones. Performing percutaneous nephrolithotomy (PCNL) on patients with spina bifida presents unique challenges due to the anatomical deformities. We present a case of a spina bifida patient with right staghorn stone and bladder stones in a previously augmented bladder. Simultaneous tubeless supine PCNL and cystolitholapaxy was successfully performed. This case highlights the versatility of the supine position in managing complex stones in patients with spina bifida.