Dengue is one of the crucial diseases in human-caused by dengue virus (DENV) infection. However, the development of DENV antiviral is often facing a problem because no effective drug to treat infection caused by all DENV serotypes. The inhibition of host protein involved in DENV life cycle can be a potential approach in dengue drug discovery, and also avoiding antiviral resistance. Endoplasmic Reticulum (ER) alpha-glucosidase II is one of the target host protein in DENV endoplasmic reticulum that plays an important role in the maturation process of DENV envelope glycoprotein. In this research, pharmacophore-based virtual screening and molecular docking simulations were performed to find ligand that has potential to inhibit alpha-glucosidase II activity. About 67,609 natural products from InterBioScreen (IBS) database were used in the simulation as ligands with alpha-glucosidase II as the protein target. After subjected to Lipinski’s Rule of Five, drug-likeness, nasty functions, and toxicity screening using DataWarrior software, 17,462 ligands were obtained. The pharmacophore features for molecular docking simulation was obtained from Protein-Ligand Interaction Fingerprint (PLIF) analysis using eight alpha-glucosidase II protein with different ligands. Based on virtual screening, rigid, and flexible docking simulations using Molecular Operating Environment (MOE) software, 32 ligands have lower Gibbs free binding energy (ΔGbinding) compared to the standards. The best ligand, namely STOCK1N-86400 which belongs to alkaloid derivative, showed the exceptional ligand interaction and had the lowest ΔGbinding of - 10.276 kcal/mol. The ligand was identified to have a binding interaction with amino acid Asp564 and Asp640 in alpha-glucosidase II catalytic site. The STOCK1N-86400 was also identified to have good pharmacological properties after subjected to ADME-tox test using Toxtree, SwissADME, admetSAR, and pkCSM software.