By virtue of the most fatal pandemic disease, Malaria, about a million individuals reach lethality globally every year and with ever consummating drug-resistant malarial parasite species, there occurred a coercive demand for the identification of incipient drug targets. Here we have evaluated a new drug target in phospholipid metabolic pathway such as Phosphocholine cytidylyltransferase (PfCCT) which is involved in the synthesis of Phosphatidylcholine, a class of phospholipids that significantly sways the developmental aspects of malarial parasite along with its replication and longevity within human red blood cells. The Objective of Present study is to identify potential lead molecule against PfCCT through docking with homology model of our target protein and common pharmacophore approach of our target inhibitor molecules. In this study, we computationally modeled the structure of PfCCT using Molsoft and validated by PROCHECK, ProSA and RMSD. With the finally refined target structure we performed docking using GOLD 3.1 and pharmacophore studies using Discovery Studio with 12 natural compounds. The predicted homology model of PfCCT is reliable. On the basis of the docking scores and pharmocophoric features, we have identified the compounds Amodiaquine and Quinidine showing better binding affinity towards PfCCT respectively with good fitvalues. In conclusion, the two compounds Amodiaquine and Quinidine shows potential inhibition against PfCCT respectively as targeted for malaria and also having better pharmacophoric features that could aid in the design of new lead molecules.