To date no study has examined time trends in adolescent consumption of sugar-sweetened beverages and energy drinks, or modelled change in inequalities over time. The present study aimed to fill this gap by identifying historical trends among secondary school students in Wales, United Kingdom. The present study includes 11–16 year olds who completed the Health Behaviour in School-aged Children (HBSC) survey and the Welsh School Health Research Network (SHRN) survey between 1998 to 2017. Multinomial regression models were employed alongside tests for interaction effects. A total of 176,094 student responses were assessed. From 1998 to 2017, the prevalence of daily sugar-sweetened beverage consumption decreased (57% to 18%) while weekly consumption has remained constant since 2006 (49% to 52%). From 2013 to 2017, daily consumption of energy drinks remained stable (6%) while weekly consumption reports steadily decreased (23% to 15%). Boys, older children and those from a low socioeconomic group reported higher consumption rates of sugar-sweetened beverages and energy drinks. Consumption according to socioeconomic group was the only characteristic to show a statistically significant change over time, revealing a widening disparity between sugar-sweetened beverage consumption rates of those from low and high socioeconomic groups. Findings indicate a positive shift in overall consumption rates of both sugar-sweetened beverages and energy drinks. Adolescents from a low socioeconomic group however were consistently shown to report unfavourable sugar-sweetened beverages consumption when compared to peers from high socioeconomic group. Given the established longer term impacts of sugar-sweetened beverage and energy drink consumption on adolescent health outcomes, urgent policy action is required to reduce overall consumption rates, with close attention to equity of impact throughout policy design and evaluation plans.