Objective: The aim was to conduct an empirical assessment of the measurement properties of the preference-based Child Health Utility 9D (CHU9D) versus the non-preference-based Pediatric Quality of Life Inventory (PedsQL)™ 4.0 Short Form 15 Generic Core Scales (referred to as ‘PedsQL’) in an Australian community-based sample of adolescents. Methods: An online survey including the CHU9D, the PedsQL, a self-reported general health question, and socio-demographic questions was administered to adolescents (aged 15–17 years). Descriptive summary statistics and psychometric analyses were conducted to assess levels of agreement and convergent validity between the instruments. Results: A total of 775 adolescents (mean ± SD age 15.8 ± 0.8 years) completed the survey. The mean ± SD scores of the CHU9D and the PedsQL were 0.72 ± 0.22 and 72.86 ± 16.56, respectively. For both instruments, there were significant differences in health-related quality of life scores according to self-reported health status and socio-economic status. Overall, both the Spearman’s correlation (r = 0.63) and the intraclass correlation coefficient (0.77) suggested a high level of agreement. Conclusions: The findings indicate good levels of agreement overall between the CHU9D and PedsQL and provide further support for the validity of the application of the CHU9D in the economic evaluation of adolescent health care treatment and service programmes.