The imposition of the stresses of climate change (higher temperatures and in many regions lower rainfall) on existing stressors, such as habitat loss and degradation, will increase pressures on native fauna already experiencing declines. We focused on assessing how the ‘Big Dry’ (severe drought, 1997–2010) in south-eastern Australia affected populations of a small marsupial carnivore, the yellow-footed antechinus (Antechinus flavipes), in box-ironbark forests, which suffer a range of anthropogenic disturbances. Trapping of the mammal was conducted on 136 (0.25 ha) sites in two box-ironbark forests in 2004, 2005 and 2011 (46 or 64 sites per year). Capture rates of all distinct individuals, males and second-year females with suckled teats, and the number of suckled teats were positively associated with rainfall in the previous September (time of lactation and deposition of young in nests). Despite differences between forests in capture rates of all individuals, the positive effect of rainfall was evident in both forests. Populations in one forest, Chiltern, were substantially larger than other locations surveyed in 2004 and 2005, yet crashed to small numbers in 2011. This crash was most likely due to low rainfall in the preceding years including the lowest recorded annual rainfall (2006), below-average annual rainfall (2007, 2008 and 2009) and well-below-average rainfall in September (2006, 2007 and 2008). The predicted drying and warming climate in south-eastern Australia and habitat loss and degradation pose a threat to the viability of the yellow-footed antechinus in box-ironbark forests. An integrated approach to small-mammal management is necessary given that the region may be facing additional losses, especially during droughts, to those already experienced since the early 1800s. Our work emphasizes the need to identify specific effects of stressors on vital demographic characteristics of species.