In pediatric cardiac surgery patients, when an artifact due to overdamping or to underdamping is suspected to affect the invasive arterial blood pressure (IABP) measure and waveform, a check against non-invasive blood pressure (NIBP) could be useful. In this study, we aimed to retrospectively analyze the differences between IABP (single site) and NIBP, measured at four limbs in children admitted to pediatric cardiac intensive care unit. Overall, 51 patients were enrolled for a total of 546 measurements. Average differences between IABP and NIBP measurements were relatively high with 42% of differences laying within the benchmark value of ± 5 mmHg. Differences on the measures on one limb vs. the others for systolic, diastolic, and mean arterial pressures were not significant (p = 0.16, 0.98, and 0.89, respectively). The systolic invasive–non-invasive differences were generally negative and diastolic and mean ones were generally positive. Correlations of clinical variables with arterial pressures at different sites were rather weak: age was associated with increased IABP–NIBP differences, whereas heart rate and vasoactive-inotropic score showed inverse correlation with IABP–NIBP deltas. Average systolic, diastolic, and mean IABP–NIBP differences of 45 patients without underdamping artifacts were not significantly different compared to those of 6 patients with underdamping (p = 0.17, 0.84, and 0.08, respectively). In conclusion, a wide bias can be detected in post-cardiac surgery children between IABP and NIBP pressures in more than half of measurements, with underdamping/resonance incidence being relatively low. Measurement of both methods without a limb preference should be considered in cardiac surgery children.