Caspases are enzymes which are the main pathway for apoptosis. Any irregulation in their functions causes increase or decrease cell death which result in autoimmune or cancer respectively. Structure-based pharmacophore drug discovery method was used to discover selective inhibitors for Caspase-9 as the initiator Caspase through effective pathway in Alzheimer’s disease, through virtual screening. A pharmacophore model was developed by investigating essential interactions between the reported potent inhibitors employing a docking analysis methodology. After pharmacophore virtual screening, 9 compounds from both National Cancer Institute (NCI) and ZINC databases were filtered as potent inhibitors of Caspase-9. The efficiency of the discovered compounds was further monitored by docking studies.