In this article, the transient behavior of the heat transfer in the fuel element of a pebble bed modular reactor is presented. The pebble fuel is a heterogeneous system that is made up of microsphere constitutes by UO2, pyrolytic carbon, and silicon carbide mixed with graphite. To describe the anomalous thermal diffusion in this complex system, a fractional constitutive law of non-Fourier type is applied. The numerical results of the temperature distribution with fractional model were compared with the classical heat transfer model. The numerical simulations during transient behavior of the anomalous thermal diffusion process are presented in the heterogeneous pebble fuel for different anomalous diffusion exponents.