Autoimmune lymphoproliferative syndrome (ALPS) is a rare inborn error of immunity caused by defective FAS-mediated apoptosis, resulting in chronic nonmalignant lymphoproliferation, autoimmune cytopenias, and an increased lifetime risk of lymphoma. Because its manifestations overlap with hematologic malignancies and other immune dysregulation disorders, diagnosis is frequently delayed. We report a 21-month-old girl who presented with recurrent viral illnesses, normocytic anemia, transient thrombocytopenia, monocytosis, and massive splenomegaly. Initial evaluation focused on excluding acute leukemia, lymphoma, juvenile myelomonocytic leukemia, hemolytic anemia, and other causes of pediatric splenomegaly. Bone marrow biopsy, flow cytometry, cytogenetic analysis, and fluorescence in situ hybridization demonstrated no evidence of malignancy or myelodysplasia. Persistent reticulocytosis and splenomegaly prompted evaluation for an underlying immune dysregulation syndrome. Next-generation sequencing identified a pathogenic FAS variant, establishing the diagnosis of ALPS, with supporting findings of elevated vitamin B12, interleukin-18, borderline expansion of TCR??? double-negative T cells, and persistent splenomegaly. A concurrent TNFRSF13B variant of uncertain significance was also identified. The patient’s father was subsequently found to carry the same FAS variant but remained asymptomatic, illustrating the incomplete penetrance and variable clinical expressivity characteristic of haploinsufficient FAS mutations. The patient was treated with mycophenolate mofetil as a steroid-sparing agent, resulting in reduction of splenomegaly and stable hematologic parameters over six months of follow-up. This case highlights the importance of considering ALPS in young children with unexplained cytopenias and splenomegaly after malignancy has been excluded and emphasizes the role of early genomic testing in establishing the diagnosis, guiding therapy, facilitating genetic counseling, and informing long-term surveillance.