Objective: To assess the cost-effectiveness of a brief cognitive behavioural intervention for patients with medically unexplained physical symptoms (MUPS) provided by a mental health nurse practitioner (MHNP) in primary care in comparison with usual care. Methods: We performed an economic evaluation from a societal perspective alongside a cluster randomised controlled trial with 12 months follow-up. The primary outcome was quality-adjusted life-years (QALYs). Secondary outcomes were the RAND-36 physical component summary score (PCS), somatic symptom severity (Patient Health Questionnaire (PHQ-15), and anxiety and depression symptoms (Hospital Anxiety and Depression Scale (HADS)). Missing data were imputed using multiple imputation. We used non-parametric bootstrapping to estimate statistical uncertainty. The bootstrapped cost-effect pairs were used to estimate cost-effectiveness planes and cost-effectiveness acceptability curves. Results: Mean total costs in the intervention group were significantly lower than in the usual care group (mean difference − 2300€, 95% CI -3257 to −134). The mean difference in QALYs was 0.01 (95% CI −0.01 to 0.04), in PCS 2.46 (95% CI 1.44 to 3.47), in PHQ-15 -0.26 (95% CI -0.81 to 0.28), and in HADS -0.07 (−0.81 to 0.67). At a willingness to pay of 0 € per additional unit of effect, the probability of the intervention being cost-effective was 0.93 for QALYs and 0.92 for PCS, PHQ-15 and HADS scores. Conclusion: Our intervention is cost-effective compared to usual care for patients with MUPS. Implementation of the intervention has the potential to result in a significant decline in costs. However, large scale implementation would require increased deployment of MHNPs.