We present a theoretical analysis of an additional nonlinear phase shift of backward Stokes wave based on stimulated Brillouin scattering in the system with a bi-directional pumping scheme. We optimize three parameters of the system: the numerical aperture, the optical loss and the pumping wavelength to minimize an additional nonlinear phase shift of backward Stokes waves due to stimulated Brillouin scattering. The optimization is performed with various Brillouin pump powers and the optical reflectivity values are based on the modern, global evolutionary computation algorithm, particle swarm optimization. It is shown that the additional nonlinear phase shift of backward Stokes wave varies with different optical fiber lengths, and can be minimized to less than 0.07 rad according to the particle swarm optimization algorithm for 5 km. The bi-directional pumping configuration system is shown to be efficient when it is possible to transmit the power output to advanced when frequency detuning is negative and delayed when it is positive, with the optimum values of the three parameters to achieve the reduction of an additional nonlinear phase shift.