Value of the Data •This dataset, including raw data, can be used by other research groups interested in TBEV interactions with host cells, host defense mechanism to the infection, etc., or focused on the interaction of TBEV with immune cells. •Antigen-presenting cells (macrophages) play an important role in the initial phase of the development of tick-borne encephalitis, being the main reservoir of the virus during an incubation period and at the stage of early viremia. This determines the prospects of their use in the biomedical studies. •Comparative analysis of early and late stages of TBEV infection in PMJ2R cells provided a set of proteins for which their biological role should be further evaluated.