Abstract Background Antibiotic resistance to Staphylococcal infections has prompted the pharmaceutical and scientific community to consider alternate treatments. Propolis is a natural substance produced by honey bees (Hymenoptera: Apis mellifera) from the exudates of different plants. The aim of the current study was to evaluate the antibacterial activity of ethanolic extracts of Pakistani bee propolis (PBP) against Staphylococcus aureus in both in vitro and in vivo modeling. Methods The propolis sample was collected from the Kohat district and dried in the dark until processing. The antibacterial activity of the propolis extract was examined using the agar well diffusion method. The S. aureus culture was incubated on Mueller–Hinton agar media. Five different concentrations of propolis, 100, 200, 350, 500, and 650 μg/ml, were used. Gentamicin disc was used as a positive control. For in vivo assay, BALB/c mice with an average weight of 30 g were purchased. Bacteria were inoculated into mice by the tape stripping technique. After abscess formation, mice were treated with propolis extract. Results The mean zone of inhibition and standard deviation for each concentration were 17 ± 0.816 at 650 μg/ml, 14.6 ± 0.471 at 500 μg/ml, 12 ± 1.41 at 300 μg/ml, 9.6 ± 0.942 at 200 μg/ml, and 2.3 ± 0.471 at 100 μg/ml of the propolis extract against S. aureus. It was observed that by increasing the concentration of the propolis extract, the antibacterial and antioxidant activities also increased. The extracts showed less antibacterial potential compared to gentamicin. The abscess size was also decreased in mice groups treated with the propolis extract topically and orally in comparison with the untreated mice group. Conclusions To the author’s best knowledge, this study is the first attempt to demonstrate that an ethanolic PBP extract has antibacterial potential against S. aureus-induced infections.