The Cerrado biome is a complex of open forests, gallery forests and savanna vegetation that harbours about 60 species of small mammals. Despite the frequent occurrence of fire in this habitat, few studies have analysed its effects on the small mammal communities in the Cerrado. The purpose of this study was to compare small mammal communities of two Cerrado areas with different fire frequencies (2–3 years or more than 18 years since the last fire). Species diversity, species composition, and relative abundance of the most common species of these communities were analysed in both areas before and after fire. One trapping grid was established in each of the two areas. These areas were sampled monthly or bi-monthly during 1 year before and 1 year after prescribed fires. Both areas had communities with similar species composition, but the protected site had more species, before and after fire (seven and eight, respectively), than the frequently burned site (five and six species, respectively). Both sites showed significant post-fire changes for a short time period (3 months), but only the area that had been protected against fire for more time showed significant post-fire changes in relative abundance of the most common species (the murid rodents Bolomys lasiurus, Calomys callosus, C. tener, Oryzomys subflavus, and Thalpomys cerradensis) for the 1 year following fire. Overall diversity tended to be greater in the protected site both before and after fire. Species composition and diversity indices of the small mammal communities were relatively unaffected by the fires. Thalpomys cerradensis, however, appeared to use only areas that burn frequently and C. callosus showed an immediate post-fire increase in population size in both areas, contrasting with a simultaneous decrease in number of B. lasiurus.