Among the possible venous thromboembolic events in nephrotic syndrome, renal vein thrombosis and pulmonary embolism are common, while portal vein thrombosis (PVT) is rare. This report describes a 26-year-old man with histologically proven minimal change disease (MCD) complicated by PVT. The patient presented with epigastric pain and edema. He had been diagnosed with MCD five months earlier and achieved complete remission with corticosteroids, which were discontinued one month before the visit. Full-blown relapsing nephrotic syndrome was evident on laboratory and clinical findings, and an abdominal computed tomography revealed PVT. He immediately received immunosuppressants and anticoagulation therapy. An eight-week treatment resulted in complete remission, and a follow-up abdominal ultrasonography showed disappearance of PVT. In conclusion, PVT is rare and may not be easily diagnosed in patients with nephrotic syndrome suffering from abdominal pain. Early recognition of this rare complication and prompt immunosuppression and anticoagulation therapy are encouraged to avoid a fatal outcome.