Ebola virus disease (EVD) is a virulent disease which responsible for 11,325 deaths in the last EVD outbreak in 2014. Although the virus has been known for more than 40 years, no approved drug or treatment can efficaciously cure this disease. Thus, Ebola remains as one of the most challenging health problems worldwide. The most lethal EVD is caused by Ebola virus (EBOV), which classifies into Filoviridae family. EBOV genes encode seven polyproteins, one of them is VP40, the most abundant protein in the viral layer. VP40 is essential for the viral assembly and budding process of EBOV. Hence, makes it viable as the drug target for treating this malignant disease. In this research, a total of 3,429 Indonesian natural product compounds, gathered from various sources, underwent a series of virtual screening and docking simulations to predict their binding affinity against EBOV VP40. Additionally, the oral bioavailability and druglikeness predictions were also conducted to identify the molecular properties of the selected drug candidates. As the result, we discovered two compounds (mesuaferrone B and euphorbianin) that are highly potential to be developed as EBOV VP40 inhibitor.