A new solution method for the diffusion depletion equation is presented. Space-dependent macroscopic cross sections are represented in the framework of a finite element basis, and the finite element method is extended to deal with these space-dependent cross sections. This method has been implemented in the NEPTUNE system of reactor calculation to be applied to two- and three-dimensional depletion calculation of large reactors. Numerical calculations are presented, and comparisons are performed with standard methods.