Human impacts on marine ecosystems are at unprecedented levels, and the ability of scientists and managers to rapidly respond to environmental emergencies amid high uncertainty is particularly important for threatened species. The Critically Endangered red handfish (Thymichthys politus) faces imminent extinction due to multiple existing threats including small, fragmented population, and severely degraded habitat. Predicted marine heatwave and localised high atmospheric temperatures in summer 2023-24 at the last remaining site in south-eastern Tasmania triggered an emergency intervention strategy to safeguard the species from extinction. Following an expert-led workshop which incorporated population, habitat and marine heatwave forecasting data, the decision was made to temporarily extract a portion of the population for ex situ management during the predicted heat stress period. The intervention was coordinated and implemented within a 5-week period, where 25 handfish were moved into captivity. We discuss the challenges and outcomes, using survival, disease, and temperature data from sites to assess the potential impact of the heatwave and success of this management option.