Background Critical limb ischaemia is a severe stage of lower limb peripheral artery disease which can lead to tissue loss, gangrene, amputation and death. FlowOx™ therapy is a novel negative-pressure chamber system intended for home use to increase blood flow, reduce pain and improve wound healing for patients with peripheral artery disease and critical limb ischaemia. Methods A Markov model was constructed to assess the relative cost-effectiveness of FlowOx™ therapy compared to standard care in lower limb peripheral artery disease patients with intermittent claudication or critical limb ischaemia. The model used data from two European trials of FlowOx™ therapy and published evidence on disease progression. From an NHS analysis perspective, various FlowOx™ therapy scenarios were modelled by adjusting the dose of FlowOx™ therapy and the amount of other care received alongside FlowOx™ therapy, in comparison to standard care. Results In the base case analysis, consisting of FlowOx™ therapy plus nominal care, the cost estimates were £12,704 for a single dose of FlowOx™ therapy per annum as compared with £15,523 for standard care. FlowOx™ therapy patients gained 0.27 additional quality adjusted life years compared to standard care patients. This equated to a dominant incremental cost-effectiveness ratio per QALY gained. At the NICE threshold WTP of £20,000 and £30,000 per QALY gained, FlowOx™ therapy in addition to standard care had a 0.80 and 1.00 probability of being cost-effectiveness respectively. Conclusions FlowOx™ therapy delivered as a single annual dose may be a cost-effective treatment for peripheral artery disease. FlowOx™ therapy improved health outcomes and reduced treatment costs in this modelled cohort. The effectiveness and cost-effectiveness of FlowOx™ therapy is susceptible to disease severity, adherence, dose and treatment cost. Research assessing the impact of FlowOx™ therapy on NHS resource use is needed in order to provide a definitive economic evaluation.