Obesity is a severe public health concern that can impair brain structure and function. The potential anti-inflammatory and anti-obesogenic properties of propolis extract are beneficial in preventing brain damage after diet-induced obesity. The purpose of the study is to investigate the role of propolis extract in high-fat diet-induced obesity rats using the Lee index and brain-body weight ratio (BBWR). We divided the rats into the experimental groups as follows: CD (normal chow diet), CP (normal chow diet with propolis treatment), FD (high-fat diet), and FP (high-fat diet with propolis treatment). We administered propolis extract in CP and FP for nine weeks during 21 weeks of diet. The rat's body weight and length were measured for obesity evaluation. The brain of all experimental rats was harvested and weighed at the end of the study. We found that a chronic high-fat diet significantly increased body weight and the Lee index ( < 0.01). However, a high-fat diet significantly decreased brain weight and BBWR in rats ( < 0.05). Nine weeks of propolis extract supplementation in the FP group reduced the Lee index ( < 0.01) and slightly increased brain weight and BBWR compared to the FD group. We observed a negative correlation between brain weight and the Lee index (R = - 0.64). Therefore, we conclude that propolis extract has the potential to sustain brain health in obesity.