Flaviviruses, including dengue virus (DENV), Zika virus (ZIKV), yellow fever virus (YFV), West Nile virus (WNV), and Japanese encephalitis virus (JEV), represent significant global public health threats, with approximately 4 billion people living in areas at risk for arboviral diseases. Despite extensive efforts, no specific and effective antiviral therapy exists for flavivirus infections, and current vaccines face limitations including antibody-dependent enhancement (ADE) and imbalanced serotype protection. Plant-derived phenolic compounds (flavonoids, phenolic acids, tannins, coumarins) and terpenoids constitute the largest groups of secondary metabolites with considerable antiviral potential due to their structural diversity and multi-target mechanisms of action. This narrative review comprehensively examines the evidence regarding the antiviral effects of phenolic and terpenoid compounds against major flaviviruses, analyzing molecular mechanisms through molecular docking approaches and evaluating their potential as novel therapeutic options for zoonotic viral diseases. Mechanistically, these compounds interfere with multiple stages of the flavivirus life cycle including viral entry (envelope protein E inhibition: emodin, baicalein, Aphloia theiformis extract), polyprotein processing (NS2B-NS3 protease inhibition: ARDP, NQ4), and RNA replication (NS5 RdRp inhibition: quercetin, TERP-2, myricetin). Molecular docking studies reveal that myricetin, quercetin, baicalein, and emodin exhibit favorable binding energies to key viral proteins, with some compounds outperforming reference drugs (triptolide: -9.4 kcal/mol vs. pyrimethamine: -6.3 to -7.8 kcal/mol). In vitro evidence demonstrates that Aphloia theiformis extract achieves 90% inhibition of viral attachment with a selectivity index of 30, while terpenoid compounds (TERP-1 to TERP-3) exhibit IC50 values of 3-16 µM against DENV NS5. Despite promising results, challenges including limited bioavailability, paucity of in vivo data, and lack of clinical trials impede clinical translation. This review concludes that phenolic and terpenoid compounds represent valuable candidates for flavivirus drug development, while emphasizing the critical need for formulation optimization, synergistic studies, and rigorous clinical validation.