The long-term benefits of pulmonary annulus preservation in tetralogy of Fallot (ToF) repair in patients with a marginally small pulmonary annulus are controversial. We sought to determine whether pulmonary annulus preservation (AP) is superior to transannular patching (TAP) in lowering the risk of pulmonary valve implantation (PVI) long after the repair of ToF. Of the 255 patients who underwent total correction of ToF during infancy between January 1989 and December 2005, 114 patients (AP group = 57, TAP group = 57) were selected by propensity score matching for various preoperative variables, such as age and body weight at operation, sex, pulmonary artery size, pre-repair palliation, anatomical types of ventricular septal defect, and Z-score of pulmonary valve annulus diameter (PVA-Z). The PVA-Z of the AP and TAP groups were -2.3 ± 1.3 and -2.1 ± 1.3, respectively (p = 0.547). The time to PVI was compared between the two groups. The median follow-up duration was 146 months (AP group: 141 months, TAP group: 147 months; p = 0.191). During the follow-up periods, there were 12 reoperations for the relief of right ventricular outflow tract obstruction (RVOTO), eight PVIs, and three late deaths. While freedom from reoperation for RVOTO was comparable between the two groups (p = 0.182), freedom from PVI at postoperative 15 years was significantly lower in the TAP group than in the AP group (74 and 100 %, p = 0.015). In repairing ToF with marginally small pulmonary valve annulus, AP is associated with a lower risk of late postoperative PVI.