We present a collocation method based on fractional B-splines for the solution of fractional differential problems. The key-idea is to use the space generated by the fractional B-splines, i.e., piecewise polynomials of noninteger degree, as approximating space. Then, in the collocation step the fractional derivative of the approximating function is approximated accurately and efficiently by an exact differentiation rule that involves the generalized finite difference operator. To show the effectiveness of the method for the solution of nonlinear dynamical systems of fractional order, we solved the fractional Lotka-Volterra model and a fractional predator-pray model with variable coefficients. The numerical tests show that the method we proposed is accurate while keeping a low computational cost.