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Abstract Background There is a pressing need to offer more accessible, evidence-based psychological interventions to secondary school students who are increasingly reporting difficulties with anxiety and low mood. The aim of this pragmatic randomised multiple baseline trial is to evaluate the efficacy of a school-based counselling intervention called Knowledge Insight Tools (KIT) for reducing anxiety and low mood in UK secondary school students. KIT is a flexible intervention delivered individually and informed by cognitive behavioural therapy (CBT). Methods We will use a randomised multiple baseline design whereby young people will be randomly allocated to a baseline wait period of 3, 4, 5, 6, 7, or 8 weekly measurements, followed by receiving up to 10 weekly sessions of KIT delivered by trained, school-based practitioners. We aim to recruit 60 young people aged 11–18 who are primarily experiencing problems with low mood and/or anxiety from secondary schools across England and Scotland. We will assess child-reported anxiety, mood, and general psychological distress/coping with the Young Person’s Clinical Outcomes in Routine Evaluation (YP-CORE), recorded at each session during the baseline and intervention phases. We will also assess child-reported anxiety and low mood with the Revised Children’s Anxiety and Depression Scale (RCADS) at the beginning and end of treatment; practitioner-reported treatment fidelity with the KIT Fidelity Checklist; and practitioner-reported feasibility with an end-of-treatment Implementation Survey. We will analyse within-person and between-person change in YP-CORE scores across the baseline and intervention phases using visual analysis and piecewise multilevel growth curve models. We will also analyse pre-post changes in YP-CORE scores using randomisation tests, and reliable and clinically significant change using the RCADS scores. Discussion The KIT trial is a pragmatic, randomised multiple baseline trial aimed at evaluating a school-based, individual CBT counselling intervention for reducing anxiety and low mood in UK secondary school students. Results will directly inform the provision of KIT in school-based counselling services, as well as the growing evidence-base for school-based CBT interventions. Trial registration ClinicalTrials.gov NCT06188962. Retrospectively registered on 02/01/24.