A numerical model based on the finite element method is applied to study the thermal performance of a near-surface inter-seasonal heat storage facility. The model is validated comparing 2D numerical results with experimental measurements from a case study project undertaken by others [Carder et al 2007]. The model is used to asssess the impact that three alternative formulations of thermal fluxes at the soil surface have on the estimation of seasonal variations of temperature and stored thermal energy in the soil close to the surface. It is also shown that the choice of surface heat fluxes and initial conditions have an effect on the number of yearly cycles required to reach steady state conditions. The influence of weather conditions on the performance of the system is explored using weather data obtained from publicy available sources for three representative climates (hot, mild and cold).