Gene therapy for hemophilia B with adeno-associated virus (AAV) vector has achieved great advances over the last decade. We previously conducted a pilot study demonstrating the safety and efficacy of AAV-factor IX (FIX) Padua gene therapy (BBM-H901) in ten male participants with hemophilia B. Here we report a single-arm dose-escalation phase 1/2 trial in 6 male participants and a multicentre phase 3 trial in 26 participants with hemophilia B in China. The phase 1/2 study tested a dose of 5 × 10¹² vg kg⁻¹ (n = 6), with primary endpoints assessing dose-limiting toxicities (DLT) and adverse events (AEs). The primary endpoint was met with no DLT observed in the 10 weeks postinfusion. The most common drug-related AEs were transaminitis (33.3%), and no grade 3 drug-related AE occurred within 52 weeks postintervention. The phase 3 study tested the 5 × 10¹² vg kg⁻¹ dose, as determined in the phase 1/2 study, in 26 patients. The primary endpoint evaluated the annualized bleeding rate (ABR) after gene therapy and secondary endpoints included vector-derived FIX:C, target joint and percentage of participants with zero bleeds postgene therapy. The study met its primary endpoint as the mean (95% confidence interval (CI)) ABR within 52 weeks after BBM-H901 infusion decreased to 0.60 (0.18–1.99), and the upper limit of the 95% CI (1.99) was lower than the predefined superiority margin of 5.0 (historical ABR assumed for patients receiving prophylactic FIX treatment in China). In the phase 3 trial, the most common drug-related AEs were transaminitis as well, and the vector-derived FIX:C had a mean of 41.9 (28.7) IU dl⁻¹ at week 52. None of the participants had a target joint, and 80.8% of participants experienced zero bleeds during the 52-week follow-up. Our study supports the safety and efficacy of AAV-FIX Padua gene therapy in a large Chinese cohort. ClinicalTrials.gov registration: NCT05203679.