Fractional advection-dispersion equations, as generalizations of classical integer-order advection-dispersion equations, are used to model the transport of passive tracers carried by fluid flow in a porous medium. In this paper, we develop an implicit finite difference method for fractional advection-dispersion equations with fractional derivative boundary conditions. First-order consistency, solvability, unconditional stability, and first-order convergence of the method are proven. Then, we present a fast iterative method for the implicit finite difference scheme, which only requires storage of ( ) and computational cost of ( log ). Traditionally, the Gaussian elimination method requires storage of ( 2 ) and computational cost of ( 3 ). Finally, the accuracy and efficiency of the method are checked with a numerical example.