ObjectiveTo assess the quality of available and accessible national Clinical Practice Guidelines (CPGs) in Kenya using the Appraisal of Guidelines for Research and Evaluation II (AGREE II) tool.MethodsWe searched the websites of the Kenyan Ministry of Health, professional associations and contacted experts in relevant organisations. Our scope was guidelines on maternal, neonatal, nutritional disorders, injuries, communicable and non-communicable diseases in Kenya published in the last 5 years until 30 June 2022. Study selection and data extraction were done by three independent reviewers with disagreements resolved via discussion or with a senior reviewer. We conducted a quality assessment using the online English version of AGREE II tool across six domains. Descriptive statistics were analysed using Stata software V.17. The primary outcome was the methodological quality of the included CPGs assessed by the AGREE II tool score.ResultsWe retrieved 95 CPGs and included 24 in the analysis after screening for eligibility. The CPGs scored best in clarity of presentation and least in the rigour of development. In descending order, the appraisal scores (mean and CI) per domain were as follows: Clarity of presentation 82.96% (95% CI 78.35% to 87.57%) with all guidelines scoring above 50%. Scope and purpose 61.75% (95% CI 54.19% to 69.31%) with seven guidelines scoring less than 50%. Stakeholder involvement 45.25% (95% CI 40.01% to 50.49%) with 16 CPGs scoring less than 50%. Applicability domain 19.88% (95% CI 13.32% to 26.43%) with only one CPG scoring above 50%. Editorial independence 6.92% (95% CI 3.47% to 10.37%) with no CPG scoring above 50% and rigour of development 3% (95% CI 0.61% to 5.39%) with no CPG scoring at least 50%.ConclusionOur findings suggest that the quality of CPGs in Kenya is limited mainly by the rigour of development, editorial independence, applicability and stakeholder involvement. Training initiatives on evidence-based methodology among guideline developers are needed to improve the overall quality of CPGs for better patient care.