This study assessed cost-effectiveness of a potential anti-tick vaccine that would protect against both Lyme borreliosis (LB) and tick-borne encephalitis (TBE) in a highly endemic setting of Slovenia. A Markov model was developed to estimate cost-effectiveness of a vaccine with potential combined protection against LB and TBE from the societal perspective. The model expressed time in annual cycles, followed a target population through their lifetime, and applied an annual discounting of 3%. A target population entered the model in a susceptible state, with time dependent probabilities to acquire LB/TBE. Disease manifestations were either resolved within one cycle, or a patient developed LB/TBE sequelae. The vaccination consisted of initial immunization and one revaccination. Estimates of LB/TBE direct and indirect costs, and data on natural course of LB/TBE were obtained from Slovenian databases. Effectiveness of the vaccine with potential combined protection against LB/TBE was derived from studies on existing TBE and LB vaccines, while utility estimates were collected from various literature sources. A vaccine with potential combined protection against LB/TBE was predicted to have an incremental cost of €771,300 per 10,000 vaccinated persons, an incremental utility of 17QALYs and a base-case incremental cost-effectiveness ratio (ICER) of 46,061€/QALY. Vaccine cost, effectiveness and discount rates were identified as the most influential model parameters. A wholesale price for a vaccine shot of €9.13 would lead to cost savings followed by health gains for the vaccination strategy. The base-case ICER was below commonly accepted thresholds of cost-effectiveness, indicating that a combined LB/TBE vaccine might be a cost-effective option in Slovenia. With early Health Technology Assessment becoming increasingly important, this analysis still represents a rare example of cost-effectiveness assessment prior to market authorisation. Although obviously in such a situation some key parameters are unknown, our model sets up a tool to analyse pharmacoeconomic criteria that can help development of a cost-effective health technology, in this case a combined tick-borne diseases vaccine.