Propolis is a natural product extensively used in the drug and food industry around the world due to its medicinal properties. Among the most prominent types of propolis in the world there is the red type, and one of its production centers is the Brazilian northeast. Several biological activities from Brazilian red propolis have been studied and its efficacy has been proved; however, there are few studies that report the safety of its use. This study assessed the biochemical and morphological long‐term effects of oral consume (90 days) of Brazilian red propolis extract in Wistar rats (Rattus norvegicus, males and females). Animals were divided into three groups: vehicle (polyethylene glycol 15%), red propolis (1000 mg/kg body weight – limit test described by the OECD 408, 2018) (n=10 per group), and satellite (treated with propolis at the same dose) (n=5 per group). The satellite group had a recovery period of 30 days after daily oral gavage of 90 days, before euthanasia. During the treatment period, water and food consumption and animal weight analysis were monitored. After the experimental period, animals were euthanized and samples were collected for biochemical and histopathological analyses. Statistical analysis was performed using GraphPad Prism software version 6.0. The experimental protocol for the use of animals was approved by the Ethics Committee on Animal Use (N° 9701030418). Alterations in the weight of males treated with red propolis were observed (propolis and satellite), being the groups with lower body mass during the experiment. The red propolis group also presented an increased water intake, compared to the other groups. On the other side, the males of the satellite group presented lowest food consumption compared to the other groups. A greater relative mass of the liver in animals of red propolis groups of both sexes were noticed. However, biochemical alterations in hepatic and renal parameters were detected just in the males. Urea levels increased in the propolis and satellite groups, whereas creatinine decreased just on the propolis group. The alanine aminotransferase (ALT) levels increased on the red propolis group, and the aspartate aminotransferase (AST) values increased on the satellite group. Total protein content decreased on animals of propolis and satellite groups of both sexes. Similarly, on the propolis and satellite males, the triglycerides levels decreased. Despite the detection of biochemical alterations, no histopathological changes were detected in the organs of any group. In conclusion, Brazilian red propolis extract in a higher dose, showed no signs of immediate toxicity. However, some alterations in the relative weight of the liver and on some renal and hepatic function indicators were observed. These results, suggests that the chemical composition ‐isoflavonoids, pterocarpans and polyprenylated benzophenones‐, and the higher dosage may be strongly related to the potential sub‐chronic toxic effects observed in this study and that its action may be sex‐dependent manner.