Malaria is a devastating disease, and its management is only achieved through chemotherapy. However, resistance to available medication is still a challenge; therefore, there is an urgent need for the discovery and development of therapeutics with a novel mechanism of action to counter the resistance scourge consistent with the currently available antimalarials. Recently, plasmepsin V was validated as a therapeutic target for the treatment of malaria. The pepsin-like aspartic protease anchored in the endoplasmic reticulum is responsible for the trafficking of parasite-derived proteins to the erythrocytic surface of the host cells. In this study, a small library of compounds was preliminarily screenedin vitroto identify novel modulators ofPlasmodium falciparumplasmepsin V (PfPMV). The results obtained revealed kaempferol, quercetin, and shikonin as possiblePfPMV inhibitors, and these compounds were subsequently probed for their inhibitory potentials usingin vitroandin silicomethods. Kaempferol and shikonin noncompetitively and competitively inhibited the specific activity ofPfPMVin vitrowith IC50values of 22.4 and 43.34μM, respectively, relative to 62.6μM obtained for pepstatin, a known aspartic protease inhibitor. Further insight into the structure-activity relationship of the compounds through a 100 ns molecular dynamic (MD) simulation showed that all the test compounds had a significant affinity forPfPMV, with quercetin (-36.56 kcal/mol) being the most prominent metabolite displaying comparable activity to pepstatin (-35.72 kcal/mol). This observation was further supported by the compactness and flexibility of the resulting complexes where the compounds do not compromise the structural integrity ofPfPMV but rather stabilized and interacted with the active site amino acid residues critical toPfPMV modulation. Considering the findings in this study, quercetin, kaempferol, and shikonin could be proposed as novel aspartic protease inhibitors worthy of further investigation in the treatment of malaria.