Context. Australia has a lamentable history of mammal extinctions. Until recently, the mammal fauna of northern Australia was presumed to have been spared such loss, and to be relatively intact and stable. However, several recent studies have suggested that this mammal fauna may be undergoing some decline, so a targeted monitoring program was established in northern Australia’s largest and best-resourced conservation reserve. Aims. The present study aims to detect change in the native small-mammal fauna of Kakadu National Park, in the monsoonal tropics of northern Australia, over the period of 1996–2009, through an extensive monitoring program, and to consider factors that may have contributed to any observed change. Methods. The small-mammal fauna was sampled in a consistent manner across a set of plots established to represent the environmental variation and fire regimes of Kakadu. Fifteen plots were sampled three times, 121 plots sampled twice and 39 plots once. Resampling was typically at 5-yearly intervals. Analysis used regression (of abundance against date), and Wilcoxon matched-pairs tests to assess change. For resampled plots, change in abundance of mammals was related to fire frequency in the between-sampling period. Key results. A total of 25 small mammal species was recorded. Plot-level species richness and total abundance decreased significantly, by 54% and 71%, respectively, over the course of the study. The abundance of 10 species declined significantly, whereas no species increased in abundance significantly. The number of ‘empty’ plots increased from 13% in 1996 to 55% in 2009. For 136 plots sampled in 2001–04 and again in 2007–09, species richness declined by 65% and the total number of individuals declined by 75%. Across plots, the extent of decline increased with increasing frequency of fire. The most marked declines were for northern quoll, Dasyurus hallucatus, fawn antechinus, Antechinus bellus, northern brown bandicoot, Isoodon macrourus, common brushtail possum, Trichosurus vulpecula, and pale field-rat, Rattus tunneyi. Conclusions. The native mammal fauna of Kakadu National Park is in rapid and severe decline. The cause(s) of this decline are not entirely clear, and may vary among species. The most plausible causes are too frequent fire, predation by feral cats and invasion by cane toads (affecting particularly one native mammal species). Implications. The present study has demonstrated a major decline in a key conservation reserve, suggesting that the mammal fauna of northern Australia may now be undergoing a decline comparable to the losses previously occurring elsewhere in Australia. These results suggest that there is a major and urgent conservation imperative to more precisely identify, and more effectively manage, the threats to this mammal fauna.