We evaluated the natural course of congenital aortic valvular stenosis (AVS) and factors affecting AVS progression during long-term follow-up with echocardiography. Medical records of 388 patients with AVS were reviewed; patients with concomitant lesions other than aortic regurgitation (AR) were excluded. Trivial AVS was defined as a transvalvular Doppler peak systolic instantaneous gradient of < 25 mmHg; mild stenosis, 25–49 mmHg; moderate stenosis, 50–75 mmHg; and severe stenosis, > 75 mmHg. Median age of the patients was 3 years (range 0 day to 21 years), and 287 (74%) were male. A total of 355 patients were followed with medical treatment alone for a median of 4.6 years (range 1 month to 20.6 years), and the degree of AVS increased in 75 (21%) patients. The risk of AVS progression was higher when AVS was diagnosed in neonates (OR 4.29, CI 1.81–10.18, p = 0.001) and infants (OR 3.79, CI 2.21–6.49, p = 0.001). After the infancy period, bicuspid valve morphology increased AVS progression risk (OR 2.4, CI 1.2–4.6, p = 0.034). Patients with moderate AVS were more likely to have AVS progression (OR 2.59, CI 1.3–5.1, p = 0.006). Bicuspid valve morphology increased risk of AR development/progression (OR 1.77, CI 1.1–2.7, p = 0.017). The patients with mild and moderate AVS were more likely to have AR development/progression (p = 0.001). The risk of AR development/progression was higher in patients with AVS progression (OR 2.25, CI 1.33–3.81, p = 0.002). Newborn babies and infants should be followed more frequently than older patients according to disease severity. Bicuspid aortic valve morphology and moderate stenosis are risk factors for the progression of AVS and AR.