Background/Objectives: Rhanterium epapposum Oliv. a medicinally valuable plant traditionally used by indigenous communities to treat skin and gastrointestinal ailments and as a natural insecticide, was investigated for its phytochemical composition and diverse biological activities (antioxidant, antimicrobial, anti-inflammatory), and enzyme inhibitory (α-amylase and lipoxygenase), supported by advanced in silico analyses. Methods: Methanolic and aqueous extracts were analyzed for total phenolic, flavonoid, and tannin contents, with their metabolite profiles characterized via LC-ESI-MS/MS. Both extracts were comprehensively assessed for antioxidant, antimicrobial, anti-inflammatory, and enzyme inhibitory (α-amylase and 5-lipoxygenase) activities. Furthermore, in silico framework was applied to elucidate the binding efficiency and inhibitory potential of key bioactive compounds against selected pharmacological targets. Results: Many bioactive compounds, mainly chlorogenic and syringic acids were identified in both extracts. The aqueous extract showed higher TTC (69.61 ± 0.212 mg TAE/g extract) and TFC (23.81 ± 0.163 mg QE/g extract), while the methanolic extract was richer in phenolics and exhibited overall stronger scavenging antioxidant activity with IC50 of 14.9 ± 4.7 µg/mL (DPPH) and 35.0 ± 0.67 µg/mL (ABTS), respectively. both extracts exhibited remarkable antimicrobial activity towards ESKAPE and Candida spp. strains. Furthermore, the aqueous extract demonstrated greater, dose-dependent oedema inhibition, peaking at 100 mg/kg, and stronger α-amylase (IC₅₀ = 188 μg/mL) and lipoxygenase (IC₅₀ = 49 μg/mL) inhibition than the methanolic extract (IC₅₀ = 247 μg/mL and 188 μg/mL, respectively), though both were less potent than standard drugs. Molecular docking, MD simulations, and DFT analyses assessed phytocompounds against multiple targets. Chlorogenic acid exhibited multi-target activity, forming hydrogen bonds with Ser49, Thr121, Leu5, Ala7, Asp27 (3FYV), Asp120, Asp86, Asp218 (3Q70), Ser602, Arg415, Asn382, Arg483, Ile461, Ser508 (7Q6S), Gly249, Asp212, Tyr2 (1B2Y), and Gly249, Leu211, Asp212 (1N8Q). MD confirmed complex stability, while DFT (6-31G**) highlighted favorable electronic reactivity and stability. Conclusions: Overall, the aqueous and methanolic extracts showed complementary bioactivities, emphasizing their potential as natural therapeutic agents and viable candidates for developing new pharmacological formulations.