Epidemiological evidence shows a substantial increase in adolescent emotional problems in many countries, but reasons for this increase remain poorly understood. We tested change in emotional problems in a national sample of young people in Wales in 2013, 2017 and 2019 using identical symptom screens, and examined whether trends were accounted for by changes in youth friendship quality and bullying. The present study of 230,735 11-16-year olds draws on repeat cross-sectional data obtained on three occasions (2013, 2017 and 2019) in national school-based surveys in Wales (conducted by the School Health Research Network). Emotional problems were assessed with a brief validated symptom screen (the SCL-4). There was a significant increase in emotional problem scores between 2013 and 2019 (b[95% CI] = 1.573 [1.380, 1.765]). This increase was observed for all ages and was more pronounced for girls than boys (interaction b [95% CI] = 0.229 [0.004, 0.462]) and for young people from less affluent families (interaction b [95% CI] = -0.564[-0.809, -0.319]). Of the total sample, 14.2% and 5.7% reported frequent face-to-face and cyberbullying respectively. There were modest decreases in friendship quality and increases in rates of bullying between 2013 and 2019, but accounting for these changes did not attenuate estimates of the population-level increase in emotional problems. This study provides evidence of a substantial increase in emotional problems among young people in Wales, particularly for young people from less affluent backgrounds. Changes in bullying or friendship quality did not explain this increase.