Adeno-associated virus (AAV)-mediated gene therapy is a novel treatment promising to reduce morbidity associated with hemophilia. While multiple clinical trials continue to evaluate efficacy and safety, limited cost-effectiveness data have been published. This study compared the potential cost-effectiveness of AAV-mediated factor IX(FIX)-Padua gene therapy for severe hemophilia B patients in the United States (US) to on-demand FIX replacement and primary FIX prophylaxis, using either standard or extended half-life FIX products. A microsimulation Markov model was constructed and transition probabilities between health states and utilities were informed by published data. Costs were aggregated using a micro-costing approach. An 18-years-old till death time-horizon from the perspective of a third-party payer in the US was conducted. Gene therapy was more cost-effective than both alternatives considering a $150,000/QALY threshold. The price for gene therapy was assumed $2,000,000 in the base-case scenario, yet one of the one-way sensitivity analyses was conducted using observed manufacturing, administration and five-year follow-up cost of $87,198 for AAV-mediated gene therapy vector as derived from the manufacturing facility and clinical practice at St. Jude Children's Research Hospital. One-way sensitivity analyses showed 10/102 scenarios in which gene therapy was not cost-effective compared to alternative treatments. Notably, gene therapy remained cost-effective in a hypothetical scenario in which we estimated that the discounted factor concentrate price was 20% of the wholesale acquisition cost in the US. Probabilistic sensitivity analysis estimated gene therapy cost-effective at 92% of simulations considering $150,000/QALY threshold. In conclusion, based on detailed simulation inputs and assumptions, gene therapy was more cost-effective than on-demand treatment and prophylaxis for patients with severe hemophilia B.