Forest fires, regardless of their causes, represent one of the greatest threats to biodiversity in Brazilian protected areas. Collecting data on the causes, periods, and sites with the highest occurrence of fires allows for the adoption of more effective prevention strategies. The aim of this study was to characterize forest fires in Brazilian federal protected areas from 2006 to 2012, thus contributing to improving the knowledge of the dynamics of fires in these areas. Data were obtained from Fire Occurrence Records (ROIs, in Portuguese) available in the National Fire Information System (SISFOGO, in Portuguese) database. The total number of records found was 2,259, of which 88.2% had reported causes. Among the records with a reported cause, 42.2% correspond to unknown causes, 26.7% to debris burning, and 18.5% to arson events, which shows that the majority of fires with a known cause are the result of accidental or intentional human action. Forest fires were more frequent from July to October, with a mean of 50.6 occurrences per year, influenced by the annual precipitation distribution. Minas Gerais, Rio de Janeiro and Ceará were the states with the highest number of records, with 19.8%, 15.5%, and 12.0%, respectively. Forest fires reported without any cause information or reported as unknown cause indicate, respectively, a poor use of the tool (ROI) or an unsatisfactory expertise in identifying the cause of the fire, resulting in an obstacle for planning actions to prevent and fight forest fires in protected areas.