Ebola virus identified is an envelope, single-stranded, negative-sense RNA virus that causes severe hemorrhagic fever in humans and nonhuman primates. This virus is naturally resistant to various antibiotics, and there is no proper treatment for infection caused by this pathogen. And hence there is a need for new drugs and approaches to combat the life threatening infection caused by Ebola virus. Computer aided drug design is one of the powerful tools for discovering new drug leads against important targets. The various proteins that are essential for pathogenesis of organism are selected as targets. The viral proteins vp35 and vp40 are capable of eliciting protective immune responses to EBOV. The various functions of these proteins in pathogenesis suggested them as potential drug targets to control EBOV infections. After the proteins were selected as target, new leads were chosen from a subset of small molecules that scored well when docked in silico against targets. The drug lead molecules were evaluated for their drug likeness using “Lipinski rule of five”. The identification of appropriate drug lead molecules against these proteins has lead to a successful drug candidate against Ebola virus infection.