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Background Although transcranial magnetic stimulation (TMS) protocols are safe and efficacious therapies for treatment-resistant depression (TRD), they remain inaccessible for many people in the UK and internationally. One of the main reasons for this is a lack of evidence demonstrating their value-for-money to commissioners.Objective To assess the cost-effectiveness of repetitive transcranial magnetic stimulation therapy (rTMS) and intermittent theta-burst stimulation (iTBS) versus treatment-as-usual (TAU) for treating TRD in UK mental health care services, and to evaluate operational circumstances underpinning cost-effectiveness.Methods This economic evaluation used data from the BRIGHTMIND trial (n=255), the SMD trial (n=187) and a study-specific structured expert elicitation exercise (n=7) to model the cost and consequences for each alternative. All findings were produced on a probabilistic basis from a Markov model using Monte Carlo simulation methods. Cost-effectiveness was assessed via incremental cost-effectiveness ratios (ICERs) per quality-adjusted life-year (QALY) gained over an 18-month time horizon from the perspectives of the UK’s NHS and personal social services and from a broader societal perspective recognisant of informal care hours and productivity costs. Scenario analyses and an operational sensitivity analysis explored the impacts alternative methodologies, service delivery cases and perspectives had on base case findings.Findings From a health service perspective, rTMS and iTBS had pairwise ICERs of £12 093 and £12 959 per QALY compared to TAU, respectively. When incrementally compared, iTBS had an ICER of £16 621 versus rTMS. From a broader societal perspective, both rTMS and iTBS reduced informal care hours and were cost-saving compared with TAU. Study findings were particularly sensitive to service delivery, with the probability of being cost-effective ranging from 98% with high throughput and prompt delivery to approximately 4% with low throughput and prolonged delivery.Conclusions TMS therapies improve health, reduce informal care requirements, reduce health service utilisation and offset their costs when considered in terms of productivity losses to society. rTMS and iTBS are cost-effective and should be considered for wider clinical implementation provided they are delivered at sufficient scale and in a time-efficient manner.Clinical implications TMS can serve as a cost-effective alternative for treating moderate to severe depression after second-line treatment failure with non-psychological therapies.