Preventing species from going extinct is the major goal of conservation management. Approximately 1900 species are listed as threatened under Australia’s Environment Protection and Biodiversity Conservation Act 1999 (EPBC Act). Monitoring is a critical component of any management program and helps us to understand the status, distribution and trends of threatened species. However, recent research found that 1176 of the 1938 species listed under the EPBC Act are yet to be monitored. We developed a framework for prioritising investment in threatened species monitoring which accounts for extinction risk, surrogacy (species that are indicators for others), statistical power and monitoring cost. Applying the framework to EPBC-listed species, we found that the top 30 priority species for monitoring were 20 birds, eight plants and two mammals. Of these, 17 currently have no monitoring. Commencing monitoring programs for these species is a very high conservation priority given their risk of extinction, relative cost and potential role as surrogates for other species. Our approach can be applied to many species, is data-driven and cost-efficient. Using the framework, decision-makers can make efficient and informed prioritisation choices that maximise conservation outcomes.