Cyprinid herpesvirus 3 (CyHV‐3) can induce up to 100% mortality among carp populations. To date, there has been no safe method to prevent the consequences of the activity of CyHV‐3. Thyme is widely used in cooking due to its flavour. Both thyme and thyme essential oil (TEO) are used in traditional herbal medicine, mainly to treat respiratory system disorders. In this study, TEO containing predominantly cymene and thymol was applied to explore its antiviral effect. The toxicity of TEO was examined in MTT and crystal violet assays. The anti‐CyHV‐3 activity of TEO in the intracellular and extracellular stages of the viral replication cycle was explored in a plaque assay and TaqMan qPCR. TEO interfered with the intracellular stages of the CyHV‐3 replication cycle with selectivity indexes (SI) of around 5. It also displayed virucidal activity in a dose‐ and time‐dependent manner. Two‐hour preincubation of CyHV‐3 with TEO generated SI, ranging from 13.37 to 18.47 depending on cell line and method of examination. Preincubation of cells with TEO at a safe concentration did not decrease the intracellular viral DNA copy number, which suggests that TEO does not disturb the attachment of the virus to the cells. Further research regarding the antiviral activity of compounds of TEO is required in order to indicate the most potent molecules that could be considered candidates for application in aquaculture.