Androgenetic alopecia (AGA) is a multifactorial, progressive hair loss disorder governed by two principal pathophysiological mechanisms: the androgen-mediated 5-alpha reductase type 2 (5-AR2) enzyme pathway responsible for dihydrotestosterone (DHT) biosynthesis, and the JAK3/STAT inflammatory signalling cascade that disrupts follicular immune privilege. Current pharmacological interventions, including oral finasteride (5-AR2 inhibitor) and systemic tofacitinib (JAK inhibitor), are associated with significant adverse effects that restrict long-term patient compliance, underscoring the unmet need for safer, naturally derived therapeutic alternatives — particularly those amenable to targeted topical delivery. This study employed AutoDock Vina 1.2.0 (Vina scoring function) to investigate and compare the molecular docking binding affinities and interaction profiles of two plant-derived flavonoids — quercetin and kaempferol — against human JAK3 kinase (PDB ID: 3LXK) and human 5-alpha reductase type 2 (SRD5A2; PDB ID: 7BW1), benchmarked against tofacitinib and finasteride as respective reference standards. Receptor structures were prepared in PDBQT format, grid boxes were centred over validated active sites, and exhaustiveness was set to 8 for all docking simulations. Against JAK3 kinase, quercetin exhibited the strongest binding affinity (-9.147 kcal/mol) and kaempferol demonstrated potent affinity (-8.833 kcal/mol), both surpassing tofacitinib (-8.140 kcal/mol); interaction analysis revealed extensive Pi-Alkyl hydrophobic contacts and van der Waals engagements with key active-site residues including LEU A:1030, VAL A:911, ALA A:928, and TYR A:980. Against 5-AR2, finasteride retained positional superiority (-7.797 kcal/mol), while quercetin (-6.414 kcal/mol) and kaempferol (-6.308 kcal/mol) exhibited moderate yet pharmacologically relevant binding within the established inhibitory range for polyphenolic flavonoids. In silico ADMET profiling of quercetin as the primary lead compound demonstrated a skin permeability (log Kp: -2.735) suitable for topical enhancement strategies, alongside a favourable safety profile characterised by the absence of skin sensitisation, hepatotoxicity, and mutagenicity. These findings collectively suggest quercetin and kaempferol as promising dual-target natural lead molecules warranting further in vitro enzyme inhibition assays, ex vivo skin permeation studies, and nanocarrier-based topical formulation development for the management of androgenetic alopecia.