ObjectivesTo assess the long-term cost-effectiveness of a risk stratification pathway, compared with standard care, for detecting non-alcoholic fatty liver disease (NAFLD) in primary care.SettingPrimary care general practices in England.ParticipantsAdults who have been identified in primary care to have a risk factor for developing NAFLD, that is, type 2 diabetes without a history of excessive alcohol use.InterventionA community-based pathway, which uses transient elastography and hepatologists to stratify patients at risk of NAFLD, has been implemented and demonstrated to be feasible (NCT02037867). Earlier identification could mean earlier treatments, referral to specialist and enrolment into surveillance programmes.DesignThe impact of earlier detection and treatment with the risk stratification pathway on progression to later stages of liver disease was examined using decision modelling with Markov chains to estimate lifetime health and economic effects of the two comparators.Data sourcesData from a prospective cross-sectional feasibility study indicating risk stratification pathway and standard care diagnostic accuracies were combined with a Markov model that comprised the following states: no/mild liver disease, significant liver disease, compensated cirrhosis, decompensated cirrhosis, hepatocellular carcinoma, liver transplant and death. The model data were chosen from up-to-date UK sources, published literature and an expert panel.Outcome measureAn incremental cost-effectiveness ratio (ICER) indicating cost per quality-adjusted life year (QALY) of the risk stratification pathway compared with standard care was estimated.ResultsThe risk stratification pathway was more effective than standard care and costs £2138 per QALY gained. The ICER was most sensitive to estimates of the rate of fibrosis progression and the effect of treatment on reducing this, and ranged from −£1895 to £7032/QALY. The risk stratification pathway demonstrated an 85% probability of cost-effectiveness at the UK willingness-to-pay threshold of £20 000/QALY.ConclusionsImplementation of a community-based risk stratification pathway is likely to be cost-effective.Trial registration numberNCT02037867, ClinicalTrials.gov.