Recurrence of subaortic stenosis (SubAS) is up to ~ 19% following resection. Historically, treatment has consisted of membrane resection alone. This study investigated the effect of routine septal myectomy in addition to membrane resection. A single-center retrospective review was performed in all patients < 18 years of age undergoing membrane resection with septal myectomy for SubAS from 2003 to 2013. Demographic, perioperative, and follow-up data were collected. Freedom from reoperation and risk factors for reoperation were determined. 107 patients (median age 4.8 years) were included. There was one in-hospital death, five patients (5%) requiring pacemaker, and no iatrogenic ventricular septal defects. Follow-up was 80% complete and median follow-up was 4.9 years (range 0.5–12 years). Fourteen (16%) subjects required reoperation. Freedom from reoperation was 98% at 1 year, 86% at 5 years, and 69% at 10 years (Fig. 1). There was no difference in decrease of peak gradient between subjects who did and did not require reoperation (− 47 vs. − 40 mmHg; p = 0.59). In univariate analysis, chromosomal anomaly (hazard ratio [HR] 5.0, p = 0.02), smaller body surface area (HR 0.1, p = 0.03), and younger age at surgery (HR 0.7, p = 0.01) were significantly associated with reoperation. The routine use of myectomy with membrane excision did not result in a lower rate of reoperation or higher rates of complications compared to historical controls. Younger age, smaller size, and chromosomal anomaly were associated with increased risk for reoperation. Patients with these risk factors may benefit from more intensive long-term follow-up.