Tick-borne encephalitis virus (TBEV), belonging to the Flaviviridae family, is transmitted to humans via infected tick bites, leading to serious neurological complications and, in some cases, death. The available vaccines against the TBEV are reported to have low immunogenicity and are associated with adverse effects like swelling, redness and fever. Moreover, these vaccines are whole-organism-based, carry a risk of reactivation and potential for significant mortality. Consequently, to design a potential antigenic and non-allergenic multi-epitope subunit vaccine against the TBEV, we used an immunoinformatic approach to screen the Tick-borne virus proteome for highly antigenic CTL, HTL and B cell epitopes. The proper folding of the constructed vaccine was validated by a molecular dynamic simulation. Additionally, the molecular docking and binding free energy (−87.50 kcal/mol) further confirmed the strong binding affinity of the constructed vaccine with TLR-4. The vaccine exhibited a CAI value of 0.93 and a GC content of 49%, showing a high expression capability in E coli. Moreover, the analysis of immune simulation demonstrated robust immune responses against the injected vaccine and clearance of the antigen with time. In conclusion, our vaccine candidate shows promise for both in vitro and in vivo analyses due to its high immunogenicity, non-allergenicity and stable interaction with the human TLR-4 receptor.