Retrospective electrocardiogram-gated, 2D phase-contrast (PC) flow MRI is routinely used in clinical evaluation of valvular/vascular disease in pediatric patients with congenital heart disease (CHD). In patients not requiring general anesthesia, clinical standard PC is conducted with free breathing for several minutes per slice with averaging. In younger patients under general anesthesia, clinical standard PC is conducted with breath-holding. One approach to overcome this limitation is using either navigator gating or self-navigation of respiratory motion, at the expense of lengthening scan times. An alternative approach is using highly accelerated, free-breathing, real-time PC (rt-PC) MRI, which to date has not been evaluated in CHD patients. The purpose of this study was to develop a 38.4-fold accelerated 2D rt-PC pulse sequence using radial k-space sampling and compressed sensing with 1.5 × 1.5 × 6.0 mm(3) nominal spatial resolution and 40 ms nominal temporal resolution, and evaluate whether it is capable of accurately measuring flow in 17 pediatric patients (aortic valve, pulmonary valve, right and left pulmonary arteries) compared with clinical standard 2D PC (either breath-hold or free breathing). For clinical translation, we implemented an integrated reconstruction pipeline capable of producing DICOMs of the order of 2 min per time series (46 frames). In terms of association, forward volume, backward volume, regurgitant fraction, and peak velocity at peak systole measured with standard PC and rt-PC were strongly correlated (R(2) > 0.76; P < 0.001). Compared with clinical standard PC, in terms of agreement, forward volume (mean difference = 1.4% (3.0% of mean)) and regurgitant fraction (mean difference = -2.5%) were in good agreement, whereas backward volume (mean difference = -1.1 mL (28.2% of mean)) and peak-velocity at peak systole (mean difference = -21.3 cm/s (17.2% of mean)) were underestimated by rt-PC. This study demonstrates that the proposed rt-PC with the said spatial resolution and temporal resolution produces relatively accurate forward volumes and regurgitant fractions but underestimates backward volumes and peak velocities at peak systole in pediatric patients with CHD.