Background The rapid evolution of viral pathogens, particularly SARS-CoV-2, necessitates the development of novel antiviral agents with diverse mechanisms of action. Methods This study investigates the antiviral potential of Cymbopogon citratus methanol extract using integrated in vitro and in silico approaches, with a focus on its mechanism of action. Phytochemical analysis revealed a composition rich in terpenoids, phenolics, and flavonoids. Results The extract demonstrated potent antiviral activity in Vero E6 cells, with a CC₅₀ of 458.1 µg/mL, an IC₅₀ of 20.31 µg/mL, and a selectivity index (SI) of 22.56, indicating a favorable safety–efficacy profile. Mechanistic assays showed that the antiviral effect is predominantly virucidal, with minimal impact on viral adsorption and intracellular replication, which was further supported by RT-qPCR analysis. Molecular docking indicated moderate binding affinities of key