Objective: Identify the prevalence of obesity in patients with chronic fatigue syndrome compared to healthy adolescents, and those identified with chronic fatigue syndrome in a population cohort. Design: Cross-sectional analysis of multiple imputed data. Setting: Data from UK paediatric chronic fatigue syndrome/myalgic encephalomyelitis (CFS/ME) services compared to data collected at two time points in the Avon Longitudinal Study of Parents and Children (ALSPAC). Patients: 1685 adolescents who attended a CFS/ME specialist service between 2004-2014 and 13978 adolescents aged approximately 13 and 16 years participating in the ALSPAC study. Main outcome measures: BMI (kg/m2), sex- and age-specific BMI Z-scores (relative to the IOTF cut-offs) and prevalence of obesity (%). Results: Adolescents who had attended specialist CFS/ME services had a higher prevalence of obesity (age 13: 9.28%; age 16: 16.43%) compared to both adolescents classified as CFS/ME in ALSPAC (age 13: 3.72%; age 16: 5.46%) and those non-CFS in ALSPAC (age 13: 4.18%; age 16: 4.46%). The increased odds of obesity in those who attended specialist services (relative to non-CFS in ALSPAC) was apparent at both 13 (OR: 2.31 (1.54 – 3.48)) and 16 years, with a greater likelihood observed at 16 years (OR: 4.07 (2.04 – 8.11)). Conclusions: We observed an increased prevalence of obesity in adolescents who were affected severely enough to be referred to a specialist CFS/ME service. Further longitudinal research is required in order to identify the temporal relationship between the two conditions.