Background: There has been a recent reported rise in prevalence of mental health problems among children in the United Kingdom, alongside increased referrals into specialist services. There is a need for up-to-date information regarding changing trends of young people’s mental health to allow for improved understanding and service planning. Objectives: This article aims to provide an overview of the current mental health and well-being of years 8, 9 and 11 secondary school–aged pupils from two large regions in the North of England. Method: This was a cohort cross-sectional study. Measures including the Strengths and Difficulties questionnaire, the EQ-5D-Y, social media use questions, and a mental health service use questionnaire were completed by participants. Results: In total, 6328 questionnaires were returned from 21 secondary schools. One in 10 participating pupils scored ‘very high’ for total mental health difficulties. Significant differences on well-being scores were found between both gender and year groups. Conclusion: In recent years, the proportion of children facing mental health problems has increased. In particular, high levels of female pupils and year 11 pupils report facing difficulties. It is important to develop targeted, accessible interventions, and to continue to collect up-to-date measures for this population.