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Introduction The Children and Young People’s Health Partnership (CYPHP) Evelina London Model of Care is a new approach to integrated care delivery for children and young people (CYP) with common health complaints and chronic conditions. CYPHP includes population health management (services shaped by data-driven understanding of population and individual needs, applied in this case to enable proactive case finding and tailored biopsychosocial care), specialist clinics with multidisciplinary health teams and training resources for professionals working with CYP. This complex health system strengthening programme has been implemented in South London since April 2018 and will be evaluated using a cluster randomised controlled trial with an embedded process evaluation. This protocol describes the within-trial and beyond-trial economic evaluation of CYPHP.Methods and analysis The economic evaluation will identify, measure and value resources and health outcome impacts of CYPHP compared with enhanced usual care from a National Health Service/Personal Social Service and a broader societal perspective. The study population includes 90 000 CYP under 16 years of age in 23 clusters (groups of general practitioner (GP) practices) to assess health service use and costs, with more detailed cost-effectiveness analysis of a targeted sample of 2138 CYP with asthma, eczema or constipation (tracer conditions). For the cost-effectiveness analysis, health outcomes will be measured using the Paediatric Quality of Life Inventory and quality-adjusted life years (QALYs) using the Child Health Utility 9 Dimensions (CHU-9D) measure. To account for changes in parental well-being, the Warwick-Edinburg Mental Well-being Scale will be integrated with QALYs in a cost–benefit analysis. The within-trial economic evaluation will be complemented by a novel long-term model that expands the analytical horizon to 10 years. Analyses will adhere to good practice guidelines and National Institute for Health and Care Excellence public health reference case.Ethics and dissemination The study has received ethical approval from South West-Cornwall and Plymouth Research Ethics Committee (REC Reference: 17/SW/0275). Results will be submitted for publication in peer-reviewed journals, made available in briefing papers for local decision-makers, and provided to the local community through website and public events. Findings will be generalisable to community-based models of care, especially in urban settings.Trial registration number NCT03461848.