This paper details health-related quality of life (HRQOL) and psychological well-being of obese children and adolescents aged 4–16 years (mean age, 10.6 years; body mass index [BMI] ≥98th percentile) upon enrolment (from January 2012 through August 2014) into a multidisciplinary community-based, 12-month obesity programme in Taranaki, which targeted indigenous people and those from most deprived households. The study cohort of 233 participants (45% Māori, 45% New Zealand European, 10% other ethnicities, 30% from the most deprived household quintile) had a mean BMI score of 3.12. At entry into the programme, parents and children completed separate versions of the HRQOL questionnaire. Parents (or the child if aged >11 years) filled out a second questionnaire to screen for behavioural and emotional difficulties, such as anxiety, sleep issues and aggression. Parents scored their children’s HRQOL and psychological well-being lower than scores in age-matched, normal-weight Australian children from the Health of Young Victorians study (mean, 63.4 vs 83.1; p<0.001). In multivariable analysis, child and parental generic scaled scores decreased in older children (β=−0.70 and p=0.031, β=−0.64 and p=0.047, respectively). Nearly half (43.5%) of all participants reported behavioural difficulties (as assessed by Achenbach’s Child Behavior Checklist [CBCL]/Youth Self Report [YSR] total score) and the prevalence of emotional and behavioural problems was 6-fold higher than normative populations (p<0.001).