Shigella sonnei is a human pathogen that causes shigellosis (dysentery) disease. Due to its resistance to currently available antibiotics in the market, shigellosis has been identified as a global crisis by the World Health Organization. Hence, there is a need to discover new drug candidates for this disease. Plant-based drug candidates have received attention for their wide variety of bioactive components and because plants are often easily accessible and inexpensive to grow. Anise seed and flaxseed essential oils have been shown to have therapeutic effects on several human diseases. In this research, the pharmaceutical potential of these essential oils was evaluated through in silico and in vitro analysis. The results of molecular docking, molecular dynamics simulation and ADMET analysis showed that isoeugenol and p-anisaldehyde from aniseed and secoisolariciresinol from flaxseed are the most promising candidates as they exhibited good binding affinities to the enzymes of the shikimate pathway and T3SS ATPase and showed promising ADMET profiles. The qualitative inhibitory assay showed that isoeugenol exerted the most inhibitory activity followed by p-anisaldehyde. The bacterium was also susceptible to SDG. The quantitative inhibition assay also indicated isoeugenol as the most potent compound with a minimum inhibitory concentration (MIC) of 0.04 mg/ml and minimum bactericidal concentration (MBC) of 0.08 mg/ml followed by p-anisaldehyde and SDG. In conclusion the in silico and in vitro assays showed that specific components of aniseed and flaxseed essential oils have potential bioactivity as drugs against S. sonnei