Context. Intermediate Polar Cataclysmic Variables (IPCV) contain a magnetic, rotating white dwarf surrounded by a magnetically truncated accretion disk. To explain their strong flickering X-ray emission, accretion has been successfully taken into account. Nevertheless, observations suggest that accretion phenomena could not be the only process behind it. An intense flaring activity occurring on the surface of the disk may generate a corona, contribute to the thermal X-ray emission and influence the system stability. Aims. Our purposes are: investigating the formation of an extended corona above the accretion disk, due to an intense flaring activity occurring on the disk surface; studying its effects on the disk and stellar magnetosphere; assessing its contribution to the observed thermal X-ray flux. Methods. We have developed a 3D magnetohydrodynamic (MHD) model of a IPCV system. The model takes into account gravity, disk viscosity, thermal conduction, radiative losses and coronal flare heating through heat injection at randomly chosen locations on disk surface. To perform a parameter space exploration, several system conditions have been considered, with different magnetic field intensity and disk density values. From the results of the evolution of the model, we have synthesized the thermal X-ray emission. Results. The simulations show the formation of an extended corona, linking disk and star. The flaring activity is capable of strongly influencing the disk configuration and possibly its stability, effectively deforming the magnetic field lines. Hot plasma evaporation phenomena occur in the layer immediately above the disk. The flaring activity gives rise to a thermal X-ray emission in both the [0.1 − 2.0] keV and the [2.0 − 10] keV X-ray bands.Conclusions. An intense coronal activity occurring on the disk surface of an IPCV can affect the structure of the disk depending noticeably on the density of the disk and the magnetic field of the central object. Moreover, the synthesis of the thermal X-ray fluxes shows that this flaring activity may contribute to the observed flickering thermal X-ray emission.