**Title** Examining the impact of a universal social and emotional learning intervention (Passport) on internalising symptoms and other outcomes among children, compared to the usual school curriculum: Study protocol for a school-based cluster randomised trial. **Abstract** ***Background***: School-based universal social and emotional learning (SEL) interventions implemented during the transition to adolescence may be efficacious in preventing the development of mental health difficulties. This protocol describes a two-arm parallel cluster randomised controlled trial to investigate the impact of a universal SEL intervention (Passport, compared to usual provision) on internalising symptoms (primary outcome), emotion regulation, wellbeing, loneliness, social support, bullying, academic attainment, and health-related quality of life in English primary school pupils aged 9-11-years. A developer-led trial demonstrated the feasibility, acceptability, and utility of Passport; this will be the first independent trial. ***Methods***: 60 primary schools will be recruited across the Greater Manchester city-region and surrounding areas, involving 2400 pupils aged 8-9 at baseline. Schools will be allocated to the intervention arm to implement Passport over 18 weekly sessions, or the control arm to implement the usual school curriculum. Random allocation will be at school level following completion of baseline measures, with minimisation to ensure balance across trial arms in school size and free school meal eligibility. Measures will be collected at baseline, post-intervention (12 months post-baseline), and at 12 months follow-up (24 months post-baseline). The primary outcome analysis (intervention effects on internalising symptoms at post-intervention) will comprise a two-level (school, child) hierarchical linear model, following the intention-to-treat principle. Additional analyses will be undertaken to assess intervention effects on secondary outcomes; maintenance effects for all outcomes; intervention compliance moderator effects; subgroup moderator effects; and mechanisms underpinning intervention effects on the primary outcome. A mixed-methods implementation and process evaluation will examine factors that influence implementation, and a health economic evaluation will assess the cost-effectiveness of the intervention. ***Discussion***: Findings will provide educators with crucial knowledge of whether and how increasing emotion regulation through a universal intervention impacts internalising symptoms and a range of related outcomes. Findings will also inform policy related to the promotion of mental health among children and young people. If the intervention is found to be efficacious in reducing internalising symptoms and is also cost-effective, it may offer high potential as a preventative intervention for widespread implementation. **Trial Registration**: ISRCTN12875599; registered on 24th November 2022