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Introduction Equally Safe at School (ESAS) is a whole-school intervention to reduce gender-based violence (GBV) in secondary school. ESAS comprises self-assessment, student-led action group, two-tier staff training, curriculum enhancement and policy review. Schools set up key activities in Year 1 and embed them in Year 2. GBV, including sexual harassment, is common in secondary schools and disproportionately affects young women and lesbian, gay, bisexual, transgender and queer youth.Methods and analysis We will evaluate the effectiveness, cost-effectiveness, mechanisms of action and implementation of ESAS. We will recruit 36 schools across Scotland. The evaluation comprises three linked studies:Study 1: Pragmatic cluster randomised trial with 1:1 school allocation to either immediate ESAS intervention start (intervention schools) or 12-month delayed intervention start (control schools). Our primary outcome of student experience of sexual harassment will be measured at 12 months post-randomisation. Analysis of primary and secondary outcomes (student and school level) will be conducted on an intention to treat (ITT) basis comparing schools according to their original allocation.Study 2: Mixed-methods evaluation. Study 2A: Longitudinal follow-up will assess primary, secondary and intermediate outcomes at baseline, 12 months and 24 months of follow-up. Study 2B: Systems and realist-informed process evaluation will assess intervention and control school context, fidelity, dose and reach, acceptability and actor response, and how this varies by school and students. We will also assess implementation processes and mechanisms of action (beneficial or harmful), including if and how change is embedded over time, and if and how ESAS helps schools leverage other assets and resources.Study 3: Economic evaluation to assess the within-trial and longer term cost-effectiveness of ESAS.The methods include surveys in three out of six year groups (Years 2, 4 and 6) in all schools (baseline, 12 months and 24 months of follow-up); interviews with staff, students and other stakeholders; activity observations; brief surveys with key actors and analysis of trial documentation.Ethics and dissemination Ethical approval by University of Glasgow MVLS Ethics Committee (200220268). Findings will be disseminated via multiple channels to researchers, GBV and education sector stakeholders, study participants and the public.Trial registration number ISRCTN29792495