Context: Economic decision models are seldom used in developing policies for the cost-effective control of invasive species that threaten natural ecosystems. However, their potential value is shown using an example of European rabbits damaging native vegetation in Australia. Aims To better define the problem of rabbit damage, provide a sound theoretical basis for implementing cost-efficient strategies for rabbit control and show how resources available for ecosystem protection can be most effectively applied. Methods A dynamic economic decision model was developed, incorporating the costs and effectiveness of three methods for controlling rabbits among native vegetation to consider alternative management strategies. A monetary value on native vegetation was set using the 'avoided' cost of replanting trees on roadsides and from field data we described how capacity of plant communities to regenerate improves if rabbit numbers are reduced. Key results Model outputs indicated the best combinations of methods for cost-effective rabbit control and showed how the highest benefits could be gained in protecting natural vegetation. Conclusions The model provided a framework for deciding how limited resources might be used to greatest benefit for protecting native vegetation. Implications This methodology could apply to other invasive species, provided that natural assets can be given a justifiable monetary value, control costs and effectiveness can be determined and the impact of the pests on assets can be modelled as dynamic population processes.