Dengue virus is a positive-sense, single-stranded RNA virus of the Flaviviridae family. Aedes aegypti is the primary vector for transmitting dengue virus, spreading the tropical infectious illness. Currently, this virus is widespread in over 100 countries and is causing millions of new cases, which kill thousands of people each year as there is no medication available. Therefore, this study aims to identify a potential inhibitor from Dodonaea viscosa targeting the NS5 methyltransferase of the dengue virus through an in silico analysis and molecular docking approach. The NS5 methyltransferase is crucial in the host–pathogen interaction and the mechanism for this viral infection. However, Dodonaea viscosa has antiviral activity, and ligands were screened from different databases used for their preparation. Further, the molecular docking analysis was performed with the NS5 methyltransferase and screened ligands from Dodonaea viscosa. The analysis shows some promising compounds that can lead to therapeutic development, as they have high docking scores in comparison to the control used. An ADME analysis was performed for the bioactivity analysis of the selected ligands, and promising ligand profiles were found. Further, the identified potential inhibitor can be used for therapeutic development for dengue virus.