In this study, the thermal behavior of the coaxial and double U borehole heat exchangers was investigated using numerical simulations in both the long- and short-term. As a reference for borehole heat exchanger specifications, the existing coaxial and double U probes of a geothermal heat pump installed within the Horizon 2020 research project named “Cheap GSHPs” were considered. Nine years of simulations revealed that when borehole heat exchangers are subjected to a balanced thermal load, and intermittent operating modes of the ground source heat pump system are set, the coaxial pipes’ configuration provides better thermal performance due to the higher thermal capacitance of the heat-carrier fluid and the lower borehole thermal resistance. The analysis was conducted considering two different types of ground with different thermal conductivity values. As result, the more conductive ground type highlights the higher yield of the coaxial probe.