Native flora and fauna species continue to decline in the megadiverse, wealthy, economically and politically stable nation of Australia despite current efforts in policy and management. Ongoing research is examining these declines, their causes and the adequacy of current policy, but strategies for improving the outcomes for threatened species have attracted less attention. We discuss several key aspects of Australia's national threatened species management approach that potentially hinder the efficiency and effectiveness of management: the threatened species listing process is lengthy and biased; recovery plan development is resource intensive, restricted to a subset of species and often not effective; funding for threatened species management is not allocated efficiently or transparently; and management is not designed to incorporate uncertainties and adapt to changing future threats. Based on these issues we recommend four changes to current process: rationalize listing and assessment processes; develop approaches to prioritize species-based and threat-based responses cost-effectively; estimate funds required to recover species and secure longer term funding; and accommodate uncertainties and new threats into the current planning framework. Cost-effective prioritization for species and threats identifies which actions are likely to achieve the greatest benefits to species per unit cost, thereby managing more species and threats with available funds. These improvements can be made without legislative reform, additional funding or socio-economic shifts. If implemented, we believe more Australian threatened species will benefit from current efforts. Many of the challenges facing Australia are analogous to issues in other countries including the United States, Canada and the United Kingdom and these recommendations could assist in improving threatened species management.