Purpose: This study compared ethanol ablation (EA) with the Sistrunk operation (SO) with regard to feasibility, treatment efficacy, and cost-effectiveness. The goal was to evaluate whether EA could replace SO as a primary treatment modality for thyroglossal duct cysts (TGDCs).Methods: This retrospective case-control study included patients with TGDCs who were treated with either EA or SO between 2016 and 2022. The primary outcome variables evaluated were treatment efficacy (as measured by the volume reduction rate [VRR] and treatment success rate), complications, and cost-effectiveness.Results: A total of 72 patients were enrolled, with 33 in the EA group and 39 in the SO group. The procedure or operation times for the EA and SO groups were 9 and 82 minutes, respectively (P<0.001). At the final follow-up appointment, the VRR was 94.1% for the EA group and 100.0% for the SO group (P<0.001). Treatment success was achieved for 32 patients (97.0%) in the EA group and for all 39 patients (100.0%) in the SO group (P=0.458). The overall complication rates were 0.0% and 17.9% in the EA and SO groups, respectively (P=0.013). The total costs, including all treatment procedures and follow-up ultrasound examinations, were $485 and $1,081.7 for the EA and SO groups, respectively (P<0.001).Conclusion: EA demonstrates superiority over SO in terms of feasibility, safety, and costeffectiveness, while maintaining comparable treatment efficacy. Despite the need for multiple treatment sessions in approximately one-quarter of patients, EA can serve as a primary treatment modality for selected patients with TGDCs, supplanting SO.