The main objective of the study is to analyse time trends in excessive body weight (obesity, overweight) of Czech adolescents between 2002 and 2018 with regard to the socioeconomic status (SES) of adolescents’ families and to find SES-mediated correlates of adolescents’ obesity. A nationally representative sample of 29,879 adolescents (49.6% of them boys) aged 10.5-16.5 years was drawn from the Health Behaviour in School-aged Children cross-sectional, self-reported questionnaire surveys conducted in 2002, 2006, 2010, 2014, and 2018 in the Czech Republic. Across the quadrennial surveys from 2002 to 2018, we observed a clear increase in the prevalence of excessive body weight (overweight/obesity) in all SES categories of adolescents, which was most striking (p < 0.05) in adolescents with low SES (boys: +5.2/+7.5 percent points (p.p.); girls +6.3/+2.4 p.p.). When all the survey cycles were compared, the highest prevalence of overweight/obesity was evident in the low-SES adolescents in 2018, both in girls (14.9%/5.1%) and boys (20.4%/12.0%). The lower odds of obesity were significantly (p < 0.05) associated with regular vigorous physical activity, participation in organized sport. An unreasonable increase in the prevalence of obesity in adolescents with low SES suggests that national health-related and sports programmes have the least impact on children from low-SES families.