Previous studies showed the reliability of cardiac magnetic resonance imaging (cMRI) in the quantification of aortic valve stenosis in adults. The aim of this retrospective study was to assess the ability of cMRI in the quantification of congenital aortic valve stenosis (CAS) in children. Nineteen patients (mean age 14.0 ± 3.2 years, 15 boys and 4 girls) with CAS were imaged by cMRI and transthoracic echocardiography (TTE). cMRI was performed on a 1.5-Tesla MR scanner (Magnetom Avanto; Siemens Healthcare, Erlangen, Germany) using cine steady-state free precession sequences for the assessment of the aortic valve area (AVA) by MR planimetry and left-ventricular function. Phase-contrast measurement was used in cMRI to assess peak flow velocity above the aortic valve. A positive correlation was found between maximum systolic pressure gradient (MPG) as assessed by cMRI and TTE (28.9 ± 21.2 vs. 41.3 ± 22.7 mmHg, r = 0.84, p = 0.001) with a mean underestimation of 12.4 mmHg by cMRI. Only a weak correlation could be observed between AVA by cMRI and MPG at the aortic valve by TTE (r = −0.50, p = 0.029) and cMRI (r = −0.27, p = 0.40). Furthermore, a positive correlation between myocardial mass (cMRI) and MPG (TTE, r = 0.57, p = 0.01), but not between myocardial mass (cMRI) and AVA (cMRI, r = 0.07, p = 0.77), was found. The assessment of MPG by cMRI in patients with CAS is feasible with a trend toward underestimatation compared with TTE. Moreover, MPG seems to be a more accurate parameter than AVA regarding the prediction of myocardial hypertrophy.