Increasing rates of artemisinin-resistant plasmodium strains associated with malarial cases are alarming, hampering effective control of malaria. Artocarpin is a major flavonoid constituent of Artocarpus lakoocha, earlier demonstrated in-vitro potency against Malarial strains. However, efforts to elucidate the exact mechanism of interactions are still ongoing. Aiming to elucidate the probable mechanism of its anti-malarial action as Falcipain-2 (FP-2) inhibition, we investigated molecular modeling analysis. Our Molecular docking analysis for a set of 50 lakoocha bioactive compounds was realized that Artocarpin has the highest binding affinity (docking score: -6.4 Kcal/mol) against FP-2 from Plasmodium falciparum. We further accessed in-silico pharmacokinetics and toxicities for several Artocarpus lakoocha flavonoids. Our results provide critical insights into the mechanism of action of Artocarpin and other Artocarpus lakoocha flavonoids as a potential therapeutic agent (FP-2) against Malaria.