Hypericum perforatum L. is a well-documented medicinal plant traditionally used for neurological and inflammatory disorders. However, comprehensive quality standardization and mechanistic validation of its root extracts is prohibited. The present study aimed to establish pharmacognostical and phytochemical standardization for Hypericum perforatum roots and to elucidate their potential antiepileptic properties using an integrated analytical and bioinformatic approach. Pharmacognostical evaluation included physicochemical parameters, such as ash values and extractive values, supported by qualitative phytochemical screening. Regarding densitometric profiling and quantitative quercetin quantification, high-performance thin-layer chromatography was employed, ensuring batch-to-batch consistency and confirmation of marker compounds. Comprehensive characterization of metabolites proved possible by liquid chromatography–mass spectrometry analysis, which validated the physical presence of important biologically active compounds, such as rutin, quercetin, kaempferol, gallic acid, and ferulic acid. To explore the molecular basis of antiepileptic activity, identified phytochemicals were subjected to network pharmacology investigation. In network pharmacology, protein–protein interaction and enhancement investigation revealed the key targets, such as prostaglandin-endoperoxide synthase 2 (PTGS2), AKT1, epidermal growth factor receptor (EGFR), ESR1, BCL2, and SRC, which were involved in neuronal excitability, oxidative stress, inflammation, and apoptotic regulation. Integrated Kyoto Encyclopedia of Genes and Genomes and gene ontology analysis highlighted estrogen signaling, EGFR-related pathways, oxidative stress response, and kinase-mediated signaling as major mechanisms relevant to epilepsy.