Although percutaneous nephrolithotomy is generally safe, it has various complications. We present an extremely rare case in which the nephrostomy tube pierced renal parenchyma, proceeded through the right renal vein and inferior vena cava, finally reaching the right atrium. Such a tube misplaced to atrium level was firstly reported, which was safely withdrawn using a 2-step process under fluoroscopic monitoring. We also recommend the tube be marked with different color lines to maintain awareness of the tube length that has passed the peel-away sheath. Such information might help to avoid such complication.