Abstract Background Release of virus-blocking Wolbachia infected mosquitoes is an emerging disease control strategy that aims to control dengue and other arboviral infections. Early entomological data and modelling analyses have suggested promising outcomes and wMel Wolbachia releases are now ongoing or planned in 12 countries. To help inform potential scale-up beyond single city releases, we assessed this technology’s cost-effectiveness under different programmatic options. Methods Using costing data from existing Wolbachia releases, previous estimates of Wolbachia effectiveness, and a spatially-explicit model of release and surveillance requirements, we predicted the costs and effectiveness of the on-going programme in Yogyakarta City and three new hypothetical programmes in Yogyakarta Special Autonomous Region, Jakarta and Bali. Results We predicted Wolbachia to be a highly cost-effective intervention when deployed in high density urban areas with gross cost-effectiveness ratios below $1,500 per DALY averted. When offsets from the health system and societal perspective were included, such programmes even became cost saving over 10-year time horizons with favourable benefit-cost ratios of 1.35 to 3.40. Sequencing Wolbachia releases over ten years could reduce programme costs by approximately 38% compared to simultaneous releases everywhere, but also delays the benefits. Even if unexpected challenges occurred during deployment, such as emergence of resistance in the medium-term or low effective coverage, Wolbachia would remain a cost saving intervention. Conclusions Wolbachia releases in high density urban areas is expected to be highly cost-effective and could potentially be the first cost saving intervention for dengue. Sites with strong public health infrastructure, fiscal capacity, and community support should be prioritized.