Bee propolis, a resinous substance synthesized by honeybees, has been widely recognized for its antimicrobial, anti-inflammatory, and antioxidant properties. This study focused on isolating and characterizing the bioactive phytoconstituents from the methanolic extract of bee propolis while simultaneously evaluating propolis’ anticancer activity. Three bioactive flavonoids, which are apigenin, pinocembrin, and castillicetin-2, were successively separated by column chromatography and their structures elucidated by liquid chromatography-mass spectrometry (LC-MS) and nuclear magnetic resonance (NMR) spectroscopy. Using a cell viability assay, their cytotoxic activity was evaluated against the triple-negative breast cancer cell line (MDA-MB-231). It was found that castillicetin-2 had a significant cytotoxic effect at EC50 of 7.7 ± 0.6 μg/mL, apigenin at 10.82 ± 0.7 μg/mL, and pinocembrin at 25.24 ± 0.8 μg/mL. Further evaluation of the compounds revealed that these compounds, alongside their respective molecular docking, proved to have strong binding ability to benefit important targets to breast cancer, such as HER2 and CDK6, which provided more insight into these compounds being useful as potential therapeutic agents. These findings demonstrated the bioactive efficacy of the flavonoids derived from propolis and how these findings augment concerns associated with the increased attention towards the treatment of breast cancer.