Malaria is one of the infectious illnesses causing a public health burden worldwide. Plasmodium vivax (P. vivax) is the most prevalent malaria parasite in Asia and Asia Pacific. P. vivax is resistant to sulfadoxine–pyrimethamine (SP) and mefloquine. This resistance makes it extremely difficult to control and eradicate due to its ability to survive in the liver and reactivate if the person infected has a weakened immune system. Thus, this study aims to inhibit P. vivax via targeting Duffy-binding protein (DBP) with active compounds from Hops (Humulus lupulus). The inhibition of DBP is essential to reduce malaria invasion of human red blood cells. We performed a quality assessment and prediction of the active site of DBP to determine the effectiveness and prediction of ligands in inhibiting DBP. Furthermore, the mechanism and structural stability of active compounds against DBP were evaluated using a combination of molecular docking and molecular dynamics simulation and a density-functional theory (DFT) study. The results showed that rutin had the highest binding of 8.852 kcal/mol. However, after the molecular dynamics simulation was run for 50 ns, the ligand 6-prenylnaringenin via MM-PBSA calculation showed the most positive value of 106.760 kJ/mol. In addition, 6-prenylnaringenin is the most stable ligand via the analysis of root-mean-square deviation backbone (RMSDBb), root-mean-square deviation c-alpha (RMSDCa), root-mean-square fluctuation (RMSF), solvent-accessible surface area (SASA), radius of gyration (Rg), and the hydrogen bond formation. We conclude that 6-prenylnaringenin has a tight and stable bond with the targeted DBP protein. Finally, we propose the use of 6-prenylnaringenin as a potential antimalarial compound via in silico studies.