Abstract Background The present study was conducted to jointly assess some specific factors related to body fat measures using a multivariate multilevel analysis in a representative sample of Iranian mid-adolescents. Methods This study was conducted among 2538 students (1286 boys) aged 14–20 years old, who were randomly selected among 16 public high schools by multi-stage random sampling procedure from all education districts of Shiraz, Iran. Data on demographic characteristics, family history of obesity, physical activity, socio-economic (SES) variables and screen time were collected. Height, weight, triceps (TST), abdominal (AST), and subscapular (SST) skinfold thickness were measured and their body mass index (BMI) was calculated. A multivariate multilevel approach was used to analyze the factors associated with obesity measures of the TST, AST, SST at the child and district levels. Results In this study, the prevalence of overweight and obesity was estimated to be 10.2 and 5.1%, respectively. Overall, the major portion of the total variance in TST (97.1%), AST (97.7%), and SST (97.5%) was found at the child level. The results of multivariate multilevel method revealed that being girls, having a family history of obesity, and SES were significantly associated with increasing of three body fat measures (all the p-values were less than 0.05). There were significant positive associations between moderate to vigorous physical activities with AST and SST (for AST: β =2.54, SE = 1.40, p = 0.05; for SST: β =2.24, SE = 1.20, p = 0.05). Compared to children in 14–16 age group, children in age group 16–18 years had less TST (β = − 0.67, SE = 0.34, p = 0.04). Furthermore, other age groups and screen time did not play an important role in three outcome variables. Conclusions The results showed some factors that contribute to three body fat measures. Therefore, it is necessary to develop effective interventions to prevent the effects of individual and environmental undesirable factors on childhood obesity in both family and community levels.