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Introduction In 2020, the UK government established a large-scale testing programme to rapidly identify individuals in England who were infected with SARS-CoV-2 and had COVID-19. This comprised part of the UK government’s COVID-19 response strategy, to protect those at risk of severe COVID-19 disease and death and to reduce the burden on the health system. To assess the success of this approach, the UK Health Security Agency (UKHSA) commissioned an independent evaluation of the activities delivered by the National Health System testing programme in England. The primary purpose of this evaluation will be to capture key learnings from the roll-out of testing to different target populations via various testing services between October 2020 and March 2022 and to use these insights to formulate recommendations for future pandemic preparedness strategy. In this protocol, we detail the rationale, approach and study design.Methods and analysis The proposed study involves a stepwise mixed-methods approach, aligned with established methods for the evaluation of complex interventions in health, to retrospectively assess the combined impact of key asymptomatic and symptomatic testing services nationally. The research team will first develop a theory of change, formulated in collaboration with testing service stakeholders, to understand the causal pathways and intended and unintended outcomes of each testing service and explore contextual impacts on each testing service’s intended outcomes. Insights gained will help identify indicators to evaluate how the combined aims of the testing programme were achieved, using a mixed-methods approach.Ethics and dissemination The study protocol was granted ethics approval by the UKHSA Research Ethics and Governance Group (reference NR0347). All relevant ethics guidelines will be followed throughout. Findings arising from this evaluation will be used to inform lessons learnt and recommendations for UKHSA on appropriate pandemic preparedness testing programme designs; findings will also be disseminated in peer-reviewed journals, a publicly available report to be published online and at academic conferences. The final report of findings from the evaluation will be used as part of a portfolio of evidence produced for the independent COVID-19 government inquiry in the UK.Transparency declaration The lead author (the manuscript’s guarantor) affirms that the manuscript is an honest, accurate and transparent account of the study being reported; no important aspects of the study have been omitted, and any discrepancies from the study as planned have been explained.