Background Thalassemia is the most common genetic disease worldwide. Allogeneic hemopoietic stem cell transplantation is a method available to cure transfusion-dependent thalassemia major patients. Aim To report incidence of post-transplant complications and survival outcome with factors affecting it in beta thalassemia major patients. Patients & methods We concluded this retrospective study of pediatric patients (≤18 years old) who underwent their first allo-HSCT during 5 years (2015-2019), all patients received allografts from fully matched related donors. A total 115 BTM patients' data were collected and patient classified into 3 classes according to Pesaro classification. Results post-transplant complications reported in 80% of all patients with most common one was infections (63.5%) which seen more in class III (64.7%). Also, acute graft versus host disease (AGVHD), chronic GVHD, cardiovascular toxicity, endocrinopathies and graft failure were more in class III patients (35.3%, 11.8%, 11.8%, 17.6% and 11.8% respectively). While pulmonary complications, neurotoxicity and hemorrhagic cystitis reported more in class II patients (40%, 21.8% and 21.8% respectively). Three-year overall survival (OS) and thalassemia free survival (TFS) of all patients were 80% and 77.4%, with the worst outcome reported in class III patients (58.8% for both OS and TFS). Patients' age group 5-10 years and MTX included GVHD prophylaxis were associated with better survival outcomes than other factors. Conclusion Addition of Fludarabine to the conditioning regimen in class III BTM patients didn't improve the occurrence of GVHD, graft failure or survival outcomes in comparison to class I and II patients.