In order to simulate hydrogen charging and discharging cycles of mechanically loaded structures full 3D Macroscopic Rate Equation (MRE) modelling is proposed based on a finite element method (FEM). The model, implemented in the 3DS Abaqus software, uses a generalized transport equation, which accounts for mechanical fields, hydrogen transport and trapping, and their evolution with time. The influence of a-priori known thermal field has also been included. To ensure the solution convergence and the numerical stability, the trapping kinetic is introduced by using an approximation of the analytical solution the McNabb and Foster equation. Comparisons with a relevant 1D MRE code and with thermal programmed desorption (TPD) experimental results are performed on a 1D configuration to validate the model. Next, the model is used to simulate the tritium diffusion and trapping in a 2D geometry of interest in the upper plug of ITER tokamak, and results of tritium inventory are compared with an equivalent 1D calculation.