The antibacterial activities of nanoemulsions based on essential oil of thyme and its purified version on food-borne pathogens (S. Paratyphi A, S. aureus, K. pneumoniae, and E. faecalis) and spoilage bacteria of fish (P. luteola, P. damselae, V. vulnificus, E. faecalis, S. liquefaciens, and P. mirabilis) were evaluated using disc diffusion, MIC and MBC. The flavour compounds of extracted thyme oil were determined using GC-MS. Physical properties of nanomulsions (viscosity, thermodynamic stability, droplet size, and refractive index) were analysed. A scanning electron microscope (SEM) was used to observe morphology changes in the cell wall of selected bacteria. The results showed that non-purified thyme-based nanoemulsions were more effective on food-borne pathogens. Damage in bacterial cell membranes after nanoemulsion treatments were observed. Conversion of thyme oil into a nanoemulsion increased antibacterial activity and its nano-form can be used as an alternative antimicrobial agent in processed or packaged fish or food products.