Nepeta cataria, an annual herb from the Lamiaceae family, is traditionally used for treating ailments such as cancer and asthma. This study focused on isolating flavonoid derivatives from the ethanol extract of its aerial parts and examining their potential against breast cancer enzymes PI3Kα, mTOR, and AKT through molecular docking. The plant was ethanol-extracted and fractionated using n-hexane, ethyl acetate, and n-butanol. The n-butanol fraction was purified by column chromatography and preparative thin-layer chromatography, yielding two flavonoid derivatives. Their structures were identified using UV, FT-IR, and 2D NMR spectroscopy. The compounds were characterized as specific flavonoid glycosides with detailed chemical names Computational studies assessed these compounds’ interaction with breast cancer target enzymes, focusing on their inhibitory potential. ADME (absorption, distribution, metabolism, and excretion) properties and toxicity were predicted, showing no rule violations and zero toxicity. Molecular docking using Chimera and Auto Dock Vina revealed strong binding affinities, especially towards PI3Kα and AKT enzymes, with binding energies ranging from -6.7 to -8.5 kcal/mol, which were comparable or better than native ligands. The results suggest these flavonoid compounds from Nepeta cataria may effectively inhibit key enzymes involved in breast cancer, supporting its ethnomedicinal use as a potential source of anticancer agents.