Left ventricular outflow tract obstruction (LVOTO) affects survival and reoperation rates after surgical treatment of patients with interruption of the aortic arch (IAA) or coarctation of the aorta (CoA) with ventricular septal defect (VSD). The aim of the study was to determine predictors of LVOTO and to evaluate the relationship between aortic valve (AoV) morphology and the re-intervention rate. Retrospective review of patients, who underwent a conventional repair for IAA/CoA with VSD at a tertiary referral center between 1996 and 2017. The preoperative demographic data as well as pre- and post-operative echocardiographic parameters and re-interventions were reviewed. In the median follow-up of 8.3 years (range of 6.15–10.27) 5 patients (11.9%) from a total of 47 patients included in the study presented with a significant LVOTO. Four of them required reoperation after median period of 2.3 years (range of 0.3–7.9) after the initial surgery. Multivariable logistic regression identified AoV z-score (OR 0.44, p = 0.017) as predictor of LVOTO. The mean AoV z-score before the primary repair was significantly smaller in those with LVOTO as compared to those with unobstructed flow from the LV (− 3.58 ± 1.96 vs. − 1.44 ± 1.55; p = 0.0016). At 1-year follow-up, both groups showed an increase in the AoV z-score (p = 0.98). The re-intervention rate after primary repair (both surgical procedures and percutaneous interventions), either for LVOTO or reCoA, was higher in patients with AoV z-score ≤  − 3 (p = 0.007 vs. p = 0.46) and those, whose aortic annulus was less or equal than patient’s weight (kg) + 1.5 mm as compared to those with larger aortic annulus (p = 0.03 vs. p = 0.16). In patients after surgical treatment of IAA/CoA with VSD, the AoV z-score at diagnosis is a significant risk factor for reoperation for LVOTO. With age, AoV growth and z-score improvement is expected. Small AoV at diagnosis is correlated with increased rate of re-intervention for LVOTO and reCoA.