BACKGROUND: This study aimed to estimate the cost-effectiveness of a universal strategy to promote physical activity in primary care. METHODS: Data were analysed for a cohort of participants from the general practice research database. Empirical estimates informed a Markov model that included five long-term conditions (diabetes, coronary heart disease, stroke, colorectal cancer and depression). Simulations compared an intervention promoting physical activity in healthy adults with standard care. The intervention effect on physical activity was from a meta-analysis of randomised trials. The annual cost of intervention, in the base case, was one family practice consultation per participant year. The primary outcome was net health benefit in quality adjusted life years (QALYs). RESULTS: A cohort of 262,704 healthy participants entered the model. Intervention was associated with an increase in life years lived free from physical disease. With 5 years intervention the increase was 52 (95 % interval -11 to 115) per 1,000 participants entering the model (probability increased 91.9 %); with 10 years intervention the increase was 102 (42-164) per 1,000 (probability 99.7 %). Net health benefits at a threshold of £30,000 per QALY were 3.2 (-11.1 to 16.9) QALYs per 1,000 participants with 5 years intervention (probability cost-effective 64.7 %) and 5.0 (-9.5 to 19.3) with 10 years intervention (probability cost-effective 72.4 %). CONCLUSIONS: A universal strategy to promote physical activity in primary care has the potential to increase life years lived free from physical disease. There is only weak evidence that a universal intervention strategy might prove cost-effective.