We evaluate the validity of cardiac index (CI) measurements utilizing the Ultrasonic Cardiac Output Monitor (USCOM), a non-invasive Doppler ultrasound device, by comparing measurements to cardiac catheterization-derived CI measurements in patients with single-ventricle physiology. USCOM measurements were repeated three times for each patient at the beginning of a cardiac catheterization procedure for twenty-six patients undergoing elective pre-Glenn or pre-Fontan catheterization. CI was measured by USCOM and was calculated from cardiac catheterization data using Fick’s method. Bland–Altman analysis for CI showed bias of 0.95 L/min/m² with the 95% limits of agreement of − 1.85 and 3.75. Pearson’s correlation coefficient was 0.89 (p < 0.001) indicating a strong positive relationship between USCOM and cardiac catheterization CI measurements. When excluding two patients with significant dilation of the neo-aortic valve (z-score >  + 5), the bias improved to 0.66 L/min/m² with the 95% limits of agreement of − 1.38 and 2.70. Percent error of limits of agreement was 34%. There was excellent intra-operator reproducibility of USCOM CI measurements with an intra-class coefficient of 0.96. We demonstrate the use of USCOM to measure CI in patients with single-ventricle physiology for the first time, showing acceptable agreement of the CI measurements between USCOM and cardiac catheterization with a high intra-operator reproducibility.