Objective This study aimed to identify the risk factors for autoimmune hemolytic anemia (AIHA) in children with transfusion-dependent thalassemia (TDT). Methodology This cross-sectional study was conducted at the Department of Child Health, Khyber Teaching Hospital, Peshawar, Pakistan, from March 25, 2024, to September 25, 2024. A total of 300 patients under 18 years of age, diagnosed with TDT, were included in the study. Relevant demographic, clinical, and laboratory investigations were conducted for each patient, with AIHA diagnosed based on the Coombs test. Risk factors, including demographic data, disease characteristics, transfusion history, clinical factors, and laboratory parameters, were recorded and analyzed. The significance of these risk factors was assessed by using the chi-square test for categorical variables and the independent t-test for continuous variables, comparing Coombs test-compatible and incompatible patients. A p-value of less than 0.05 was considered statistically significant. Results The mean±SD age of participants in this study was 6.82±4.2 years with an age range of one to 16 years. The male gender was 56.33%. The results of the Coombs test showed that 48.66% of these children had developed AIHA. The comparison between incompatible and compatible patients at Coombs test showed that age of patients (5.87±3.93 vs. 7.68±4.28 years, p = 0.00), age at the time of diagnosis (2.21±0.99 vs. 4.64±3.03 years, p = 0.00), age at the time of first infusion (3.05±1.28 vs. 5.49±3.2 years, p = 0.00), transfusion interval < 3 weeks (48.6% vs. 37%, p = 0.04) and duration of transfusion (2.87±3.2 vs. 2.21±1.93 years, p = 0.03) were the significant risk factors in the development of AIHA. Conclusion The patient's age, age at diagnosis, age at the time of first transfusion, the transfusion interval, and the duration of blood transfusion are the significant risk factors influencing the development of AIHA., Competing Interests: Human subjects: Consent for treatment and open access publication was obtained or waived by all participants in this study. Institutional Research and Ethical Review Board, Khyber Medical College, Peshawar issued approval (218/DME/KMC). Animal subjects: All authors have confirmed that this study did not involve animal subjects or tissue. Conflicts of interest: In compliance with the ICMJE uniform disclosure form, all authors declare the following: Payment/services info: All authors have declared that no financial support was received from any organization for the submitted work. Financial relationships: All authors have declared that they have no financial relationships at present or within the previous three years with any organizations that might have an interest in the submitted work. Other relationships: All authors have declared that there are no other relationships or activities that could appear to have influenced the submitted work., (Copyright © 2024, Khan et al.)