Objectives: To investigate the association between obstructive sleep apnea (OSA) and health related quality of life (HRQOL) in children and adolescents referred to an obesity treatment clinic. In addition, we examined the association between body mass index standard deviation score (BMI SDS) and HRQOL comparing children and adolescents with overweight or obesity without OSA with a control group of children and adolescents with normal weight without OSA. Methods: This cross-sectional study included 130 children and adolescents with overweight or obesity (BMI SDS > 1.28) aged 7–18 years recruited from an obesity treatment clinic. The control group consisted of 28 children and adolescents with normal weight (BMI SDS ≤ 1.28) aged 7–18 years recruited from schools. Sleep examinations were performed using a type 3 portable sleep monitor, Nox T3. OSA was defined as apnea-hypopnea index (AHI) ≥ 2. HRQOL was measured by the Pediatric Quality of Life Inventory (PedsQL) 4.0 generic core scale. Results: A total of 56 children and adolescents with overweight or obesity were diagnosed with OSA (43%). The children and adolescents with OSA were older (p = 0.01) and had higher BMI SDS (p = 0.04) than children and adolescents without OSA. In generalized linear regression analyses adjusted for age, sex, BMI SDS and pubertal development stage there was no association between OSA or AHI and HRQOL in children and adolescents with overweight or obesity. In the analysis, including children and adolescents without OSA and the normal-weight control group, the generalized linear regression adjusted for age, sex and AHI revealed an association between BMI SDS and HRQOL (p < 0.001). Conclusion: We found no association between AHI or OSA and HRQOL in children and adolescents with overweight or obesity. However, we found an association between BMI SDS and HRQOL in children and adolescents without OSA.