Indirect and direct health-related quality of life (HRQoL) measures are intended to assess the same underlying constructs. There is evidence that the two types of assessments can show important differences. We assessed the agreement between the utilities of direct and indirect HRQoL measurements in children following pediatric intensive care unit (PICU) admission. We collected Health Utilities Index 3 (HUI-3) and Visual Analog Scale (VAS) ratings of children who were urgently admitted to the PICU of a university-affiliated pediatric hospital at ICU admission (baseline) and one month post-ICU admission. The mean (SD) VAS converted standard gamble and HUI-3 utilities were 0.82 (±0.19) and 0.70 (±0.39), respectively, at baseline (n = 51), and 0.81 (±0.15) and 0.58 (±0.39) at one month (n = 36). The VAS utilities were significantly greater than the HUI-3 utilities (p = 0.009). At baseline, the intraclass coefficient (95% confidence interval) was 0.49 (0.25–0.68), representing moderate agreement, and at one month, was 0.18 (-0.87 to 0.45), representing negligible agreement. There were significant differences between indirect and direct measures, and inconsistent agreement between utilities derived from the two measures. These data illustrate the potential impact of HRQoL assessment techniques on economic analyses used to inform health policy decision-making for pediatric critical care.