Portal vein thrombosis (PVT) is the most common cause of extrahepatic portal vein obstruction in children. Upper gastrointestinal (GI) bleeding and splenomegaly are the most common presenting features. PVT diagnosis is usually delayed in the absence of upper GI bleeding and many children undergo a hematologic work-up due to splenomegaly and signs of hypersplenism. Here, we present a case of a 2-year-old girl who had pancytopenia and splenomegaly. The hematologic work-up including a bone marrow aspirate was unrevealing and she was thought to have viral-induced bone marrow suppression and severe iron deficiency anemia. She presented 2 months later with hematemesis and abdominal CT angiography confirmed the diagnosis of PVT with portal cavernoma. Conclusion: PVT should be suspected in any child who presents with afebrile splenomegaly and signs of hypersplenism even in the absence of upper GI bleeding.