The effect of seventeen parameters (material, design and operating) on the efficiency of the long-term operation of borehole thermal energy storage (BTES) has been investigated in this paper. Global sensitivity analysis was used to determine this effect and the use of the fast meta-model to predict the thermal efficiency of BTES has also been proposed. Carrying out research on the real object using this many input parameters is impossible, therefore, the use of 3D transient simulation studies of heat and mass transport in the BTES was chosen. An efficient numerical technique, coupled with the design and analysis of the computational experiment method was used to significantly reduce the required calculation time.The results showed that the temperature of the inlet fluid during charging and discharging, as well as the thermal conductivity of the rock mass and the arrangement of the borehole heat exchangers, had a crucial impact on the efficiency of the BTES. In order to obtain high efficiency values for the BTES, it is necessary to produce the highest possible inlet fluid temperature during charging and the lowest possible temperature of the inlet fluid during discharging. The highest values of BTES efficiency can be achieved using a compact arrangement of the borehole heat exchangers (BHE spacing 1.5–3.5 m) and for low values of the thermal conductivity of the rock mass (less than 2.45 W/(m⋅K).