Introduction Chronic food protein-induced enterocolitis syndrome (FPIES) is a non-IgE gastrointestinal food allergy, typically manifesting in infancy with intermittent emesis and diarrhea, which may progress to dehydration and hypovolemic shock. Here we describe a case of chronic FPIES with previously unreported complications, including sinus venous thrombosis and intracranial hemorrhage. Case Description This female infant, the product a full term, healthy pregnancy, was initially thriving on soy formula until the 3 rd week of life when she developed progressively worsening diarrhea, emesis, and lethargy. By day of life 20, she was noted to have severe dehydration with 22% weight loss from birth. Laboratory abnormalities included anion gap metabolic acidosis, elevated lactate, hyperammonemia, hypoalbuminemia, neutrophilia with bandemia, hypereosinophilia, and thrombocytosis. Full sepsis work-up was negative as was testing for inborn errors of metabolism. Clinical course was complicated by seizures, respiratory failure, intracranial hemorrhage, and sinus venous thrombosis. Upon withdrawal of soy-based formula, laboratory abnormalities gradually improved. Resumption of feeds with extensively hydrolyzed cow's milk formula resulted in intermittent emesis. Concerned for chronic FPIES, the patient transitioned to amino acid-based formula with improvement in gastrointestinal symptoms. Discussion Here we present the first reported case of chronic FPIES complicated by sinus venous thrombosis and intracranial hemorrhage. Her diagnosis of chronic FPIES is presumptive without confirmatory food challenge; this has yet to be performed due to severity of initial presentation and patient's current young age of 2 months. This case highlights the potential severity of presentation, which may represent a barrier to timely diagnosis.