Abstract Background The Minimising Young Children’s Anxiety through Schools (MY-CATS) trial is being conducted to determine whether an online evidence-based parent-guided cognitive behavioural therapy intervention in addition to usual school practice is effective and cost-effective compared with usual school practice in reducing anxiety disorders in children aged 4–7 deemed ‘at risk’ of anxiety disorders. This update article describes the detailed statistical analysis plan for the MY-CATS trial and reports a review of the underpinning sample size assumptions. Methods and design The MY-CATS study is a two-arm, definitive superiority pragmatic parallel group cluster randomised controlled trial in which schools will be randomised 1:1 to receive either the intervention (in addition to usual school practice) or the usual school practice only. This update to the (published) protocol provides a detailed description of the study methods, the statistical principles, the trial population and the planned statistical analyses, including additional analyses comprising instrumental variable regression and mediation analysis. Trial registration ISRCTN82398107. Prospectively registered on 14 January 2021