MIRAGE syndrome is a rare, severe multisystem disorder caused by gain-of-function mutations in the SAMD9 gene and characterized by myelodysplasia, infections, growth restriction, adrenal hypoplasia, genital anomalies and enteropathy. Clinical manifestations typically emerge during early infancy and commonly include severe infections and developmental delay. We report a three-and-a-half-month-old female infant who presented with fever and pneumonia. Further evaluation revealed severe growth retardation, hypogammaglobulinemia, features of cellular immunodeficiency, and hypothyroidism. During follow-up, the patient developed cytomegalovirus infection and necrotizing enterocolitis developed. Whole-exome sequencing identified a pathogenic SAMD9 mutation, leading to a diagnosis of MIRAGE syndrome. This case highlights that MIRAGE syndrome may initially present with severe infections and gastrointestinal complications during early infancy and emphasizes the importance of early genetic evaluation in patients with similar multisystem manifestations.