Multifocal lymphangioendotheliomatosis with thrombocytopenia is a rare disease characterized by multiple cutaneous and gastrointestinal (GI) vascular lesions and thrombocytopenia refractory to platelet and blood cell transfusions. GI bleeding can become life-threatening in this condition. We report a case of multifocal lymphangioendotheliomatosis with thrombocytopenia in a male infant with isolated GI involvement, diagnosed when he was 3 months old. The patient was managed with daily aminocaproic acid, octreotide drip, and corticosteroids for 13 months after diagnosis; he had complete resolution of symptoms by 2 years of age and showed adequate height and gain by 5 years of age. This case adds to the paucity of data in the literature pertaining to the disease's phenotypic variability, long-term clinical course, and management of GI bleeding.