This study compared health-related quality of life scores between children newly diagnosed with chronic health conditions and their parents to identify potential domain discrepancies and quantified the magnitude of discrepancies during a six-month follow-up. Children aged ≥11 years and their parents completed the KIDSCREEN-27. Informant agreement was quantified using the intraclass correlation coefficient (ICC) and Bland and Altman’s limits of agreement. The proportion of child–parent dyads with a minimal clinically important difference (MCID) was computed. Children reported higher KIDSCREEN-27 scores for all subscales compared to parents. At baseline and at six months, child–parent agreement was generally low to moderate (ICC = .25–.67) and the proportion of MCID was high (36–79%). Over time, child–parent agreement improved on most domains. These exploratory findings suggest that the agreement between children newly diagnosed with chronic health conditions and their parents is low to moderate and meaningful discrepancies are common, though improve over time.