High risk pulmonary embolism is a rare and life-threatening complication following percutaneous nephrolithotomy. We report the case of a previously healthy, 44-year-old male, who developed acute pulmonary embolism following right percutaneous nephrolithotomy. On the 1st postoperative day, the patient presented with hemodynamic instability, acute respiratory distress, hypoxia, and loss of consciousness. He was urgently intubated and placed on mechanical ventilation. Clinical findings set the suspicion of pulmonary embolism with shock. Chest computed tomography scan confirmed the diagnosis. The patient underwent urgent thrombolysis in the cardiac care unit. On the 2nd postoperative day, the patient was admitted to the intensive care unit due to hemodynamic instability and fever. The postoperative course was complicated by right renal bleeding on the 3rd postoperative day, which was managed through angiography and angioembolization of the lower segmental right renal artery, followed by recurrent respiratory and urinary tract infections. The patient was transferred back to the urology department on the 66th postoperative day and was discharged seven days later.