The paper makes a comparative study of the finite element method (FEM) and the finite difference method (FDM) for two-dimensional fractional advection-dispersion equation (FADE) which has recently been considered a promising tool in modeling non-Fickian solute transport in groundwater. Due to the non-local property of integro-differential operator of the space-fractional derivative, numerical solution of FADE is very challenging and little has been reported in literature, especially for high-dimensional case. In order to effectively apply the FEM and the FDM to the FADE on a rectangular domain, a backward-distance algorithm is presented to extend the triangular elements to generic polygon elements in the finite element analysis, and a variable-step vector Grünwald formula is proposed to improve the solution accuracy of the conventional finite difference scheme. Numerical investigation shows that the FEM compares favorably with the FDM in terms of accuracy and convergence rate whereas the latter enjoys less computational effort.