Abstract: Background: Beta thalassemia is a genetic disorder causing defective beta globin chain formation, leading to ineffective erythro- poiesis and hemolysis. It has three types: thalassemia major, thalassemia intermedia, and thalassemia minor. Treatment options include blood transfusions, iron chelation therapy, and bone marrow transplantation, but new treatments like HbF inducers (e.g., hydroxyurea) and erythro- poiesis modulators are being developed. Thalidomide and hydroxyurea are also being used to manage thalassemia by increasing HbF synthesis and reducing transfusion frequency. Objective: To compare the efficacy and safety of thalidomide and hydroxyurea in beta-thalassemia patients for a period of six months. Materials and Methods: A Prospective interventional single-centre study was conducted the tertiary care hospital of southern Pakistan, from 1st September 2021 to 03rd March 2022. A total of 39 patients of beta thalassemia major and intermediate with age ranges of >10 and <30 years were enrolled in this study. 24 patients were fulfilling the study requirement. Thalidomide was started with a dose of 50 mg/day (in patients >10-13 years) while the adult dose was 100 mg /day (age >13 Years) every night. Hydroxyurea was given at 15 mg/kg /day. Pre and post-treat- ment tests were done. For assessing the safety of thalidomide and hydroxyurea biochemistry test was done along with LDH, Platelets counts, and WBCs count. The efficiency of both drugs was analyzed by hemoglobin, reticulocyte count, nucleated red blood cells, MCV, MCHC, white blood cells, and platelets. Result: Both groups showed a highly significant increment in Hb. Thalidomide treated group baseline was 6.8 ±1.3 and after 06 months 8 ±13; (p-value <0.001). Furthermore reticulocyte count was highly significantly augmented in HU treated group (p-value <0.001) Hydroxy- urea-treated group showed significant decline in NRBC with a difference of -2.3±1.1 (p-value 0.02). Moreover, the transfusion interval was more significantly increased in the thalidomide group. The hemolysis parameter, LDH significantly declined in both groups. The hydroxy- urea-treated group showed difference of -62.4±124.4 (p-value 0.03) while the thalidomide-treated group showed a difference of -64.36±32.9 (p-value 0.05). AST was only significantly decreased in thalidomide treated group. Conclusion: Among both groups, hemoglobin, RBCs and reticulocyte count levels raise in both groups while NRBCs significantly decrease in HU treated group. Moreover, transfusion interval was also significantly increased by thalidomide. It shows safety by significantly decreasing the TBIL and AST, whereas LDH was decreased in the HU-treated group. This clinical trial was registered as # NCT06239389.