Fire is a major form of disturbance in terrestrial ecosystems, mainly in tropical savannas. In these ecosystems, the effects of large wildfires are potentially high on small and relatively less mobile animals, like small mammals. We investigated the effects of an extensive wildfire (≈ 6,240 ha) in September 2011 on populations of 2 arborealscansorial small mammals—the gracile mouse opossum, Gracilinanus agilis, and the long-tailed climbing mouse, Rhipidomys macrurus—in 4 savanna woodland patches (1 burned, 3 unburned) of the highly threatened Brazilian Cerrado. We assessed population densities from 2009 to 2013 and for G. agilis, we estimated apparent survival and recapture probabilities with Cormack—Jolly—Seber models. Both species showed strong, negative fire responses, including sudden collapse and slow recovery (at least more than 1 year). These observed responses were probably a consequence of both the phytophysiognomic features of the habitat and severity of the fire with the resulting changes on the vertical structure of vegetation. The studied species of Cerrado forested formations were not as resilient to fire disturbance as typical species from savanna or temperate woodlands. As a consequence of human activities and climate changes, fire events are predicted to become larger and more frequent in the Brazilian Cerrado. Therefore, it is imperative to create new management strategies to protect forested physiognomies from fire, especially cerradão, which is very fire sensitive and has a limited and scattered distribution in the landscape.