Transfusion-related complications and lack of resources in low-to-middle-income countries have led to a search for novel therapies to reduce the need for blood transfusions in β-thalassemia patients. Hydroxyurea (HU) has demonstrated promising outcomes; additionally, thalidomide has also shown improvement in hemoglobin (Hb) levels for patients with β-thalassemia in some studies. This study presents the findings of a single-arm non-randomized trial to evaluate the efficacy of combination therapy of HU and thalidomide in children with β -thalassemia. A total of 135 patients [median age 6 (IQR 3-10) years], 77 (57%) males and 58 (43%) females were followed first using HU alone, for six months, and then using the combination of HU and thalidomide for another six months. The primary outcome was a response to therapy, as measured by the number of transfusions required and hemoglobin levels, for patients while receiving HU alone and then while using the combination therapy. Study findings showed a significant decline in blood transfusion volume (p < 0.001) and a significant increase in median Hb levels within 3 and 6 months of the combination therapy (p < 0.001). Eighty-nine (65.93%) participants were good responders, 16 (11.85%) were responders, and 30 (22.22%) were non-responders; whereas, the responders had variable genetic mutations. A total of 38 adverse events were reported which resolved on supportive treatment or temporary hold of the intervention. The combination therapy demonstrated promising results and could be considered for a diverse patient population with β-thalassemia. This trial was registered at www.clinicaltrial.gov as # NCT 05132270.