Background: Budd-Chiari syndrome is a rare entity in childhood. Antiphospholipid syndrome is an autoimmune disease characterized by the presence of thrombosis or obstetrical complications. The presentation of both diseases is rare. Currently there are few reports in the literature of this association. Case Report: A 15-year-old male patient presented with generalized pallor, Raynaud phenomenon and pain abdomen. Imaging studies reveal portal vein and splenic vein thrombosis corroborating with angiography.  Based on the thrombosis presentation, Raynaud phenomenon, aTTP prolongation, thrombocytopenia and complement consumption, diagnosis of antiphospholipid syndrome was made. He continued treatment with anticoagulation, in addition to steroid and azathioprine, presenting adequate clinical evolution. Conclusion: The seronegative antiphospholipid syndrome represents a diagnostic challenge. It´s essential to maintain a suspected diagnosis of antiphospholipid syndrome as a cause of Budd-Chiari syndrome, even in it´s seronegative presentation.