Invasive Fungal Infections (IFI) are an important complication and constitute significantly to mortality and morbidity, post Hematopoietic Stem Cell Transplant (HSCT). We report a very rare case of fungal laryngitis post HSCT in a 15-year-old girl with Thalassemia major. She received Busulphan, Cyclophosphamide and Antithymocyte Globulin (Bu-Cy-ATG) based conditioning pre Matched Sibling Donor (MSD) transplant and presented on day 10 post-transplant with hoarseness of voice progressing to stridor and respiratory obstruction. CT neck revealed laryngeal edema and she was ultimately diagnosed, by a laryngoscopy biopsy, histopathology and fungal culture to be having invasive fungal laryngitis due to Rhizopus. She responded partially to combination antifungal treatment with amphotericin B and posaconazole, family refused for laryngectomy and she was discharged with a tracheostomy tube in situ. Patient eventually succumbed due to bacterial sepsis. IFI should be considered in the differential diagnosis of unexplained symptoms post HSCT as timely intervention and treatment can save a lot of morbidity and mortality.