We present a method for including the geometric phase in quantum reactive scattering computations based on the log derivative version of the Kohn variational principle. A new variational functional is developed which includes the influence of the geometric phase through modifications in the momentum operators. The system investigated is a two-dimensional reactive scattering model which includes the vector potential induced by the magnetic field of an infinitely long solenoid. The coordinates used in this model are analogous to Jacobi coordinates used in atom-diatom systems. Some interesting features of this study include the gauge invariance of the scattering probabilities, symmetry adaptation of the wave function, and the behavior of the probability density in the presence of the geometric phase.