Plasmasphere plays an important role in the magnetospheric physics, defining many important inputs to the ionosphere from the middle to the auroral latitudes. Among them are electron thermal heat fluxes resulting from the Coulomb interaction of superthermal electrons (SE) and cold plasmaspheric electrons. These fluxes define the electron temperature at the upper ionospheric altitudes and are the input to the global ionospheric modeling networks. As was previously found from the calculation of lower energy SE and thermal heat fluxes, the knowledge of field‐aligned cold plasma distribution in the plasmasphere is a very sensitive parameter that introduces the most uncertainties in the calculation of these values. To verify the previously used SuperThermal Electron Transport code assumptions regarding plasmaspheric field‐aligned density structure ∼B(s)/Boa, we used the latest version of 3D plasmaspheric model developed by Pierrard, Botek, and Darrouzet (2021, https://doi.org/10.3389/fspas.2021.681401). Such an assumption is found to be very reasonable in the calculations of electron thermal heat fluxes entering upper ionospheric altitudes and the associated electron temperature formation for the two selected dayside and nightside electron precipitation events driven by whistler‐mode wave activity. Key Points The role of plasmaspheric field‐aligned density structure in the formation of electron thermal heat fluxes SuperThermal Electron Transport (STET) simulations of thermal heat fluxes using physics‐based 3D dynamic Belgian SWIFF Plasmasphere Model (BSPM) The BSPM simulation confirms the plasmaspheric field‐aligned density structure used in STET code and supports the heat flux calculations