Although successful hematopoietic stem cell transplantation (HSCT) can offer a cure in thalassemia major, there are only a few and noncomprehensive studies of its effect on the quality of life (QoL), as it is expected to increase the QoL by ending transfusion-related issues. Our objective was to compare the health-related quality of life (HRQoL) of transplanted and nontransplanted thalassemia major patients in a developing country. We have studied the QoL effect of HSCT in consecutively invited 50 nontransplanted and 49 transplanted patients who had received transplants from HLA matched related donors at least two years ago. PedsQL questionnaire was used for the patients under 18 years of age and World Health Organization's WHOQoL-BREF questionnaire for above 18 years of age. Higher QoL was determined in HSCT performed group surveyed in 5–18 years' age group. Detailed analysis marked the profound difference in 8–12 year subgroup, particularly in physical activity questionnaires. QoL scores in HSCT performed adult group are higher than the transfusion-dependent group, especially in physical activity domain. Transplanted adult patients rated their overall health significantly better than patients on conventional therapy. The patients who still have chronic graft versus host disease rated worse compared to those without it. In conclusion, thalassemia major patients who have undergone HSCT at least two years before assessment are not inferior to the transfusion-dependent group with regard to the QoL and have a better QoL than transfusion-dependent patients in some areas. The QoL score is better for school children and adolescents; therefore, we suggest HSCT before primary school. GVHD reduces the QoL significantly and it is obvious that GVHD prevention should be one of the primary goals of post-HSCT follow-up.