Heterozygous mutations in the interferon regulatory factor 4 (IRF4) can lead to combined immunodeficiency in humans. We report a pediatric case involving a male patient who presented with recurrent pneumonia, chronic diarrhoea, abdominal pain, and a skin rash. Laboratory evaluation revealed hypoglobulinemia and persistent B-cell lymphopenia. Genetic analysis confirmed that the combined immunodeficiency was caused by an IRF4 mutation. Given the failure of conventional therapies, the patient successfully underwent allogeneic hematopoietic stem cell transplantation (HSCT) from an unrelated donor using a reduced-toxicity conditioning regimen. Post-transplant follow-up demonstrated successful immune reconstitution and complete resolution of gastrointestinal symptoms. This case provides clinical evidence supporting HSCT as a feasible strategy to reconstitute the immune system and resolve enteropathy in patients with IRF4 mutations.