We assessed the usefulness of transthoracic Doppler-derived indexes obtained in the proximal pulmonary artery (PA) branch for estimating pulmonary vascular resistance (PVR) in 45 children with congenital heart disease (CHD) and 23 normal control subjects. The acceleration time, inflection time (InT), deceleration index, and peak velocity, which were measured from the systolic PA flow velocity curve obtained at the sites of the main PA, and right and left PA, were compared with the PVR in patients with CHD. In addition, changes in either Doppler-derived indexes or PVR during 100% oxygen administration were compared in 22 patients showing a baseline PVR ≥4.6 U/m² (high PVR). The heart-rate-corrected InT (InTc) values obtained in the left PA in the high PVR group were significantly lower than those in the main PA (4.7 ± 1.5 vs. 7.5 ± 3.0; p < 0.001). The InTc obtained from the left PA separated patients with high and low PVR (4.7 ± 1.4 vs. 9.9 ± 2.4; p < 0.001) and no significant differences in InTc were found between the low PVR and the control groups. An increase in InTc to >6 during 100% oxygen administration for the high PVR group indicated good PA reactivity with a sensitivity of 93%, specificity of 100%, and agreement of 95% (κ = 0.83). Moreover, this InTc index correlated inversely with PVR (r = –0.80). In conclusion, our method can noninvasively separate high and low PVR and assess the PA reactivity for high PVR in children with CHD.