In this paper, we have analyzed the influences of non-linear refractive index on the four-wave mixing (FWM) characteristics in semiconductor optical amplifiers (SOAs). It has been shown that the generated FWM signal characteristics can be modified due to the variation of non-linear refractive index of the SOA's medium. The wave propagation in the SOA has been modeled using the nonlinear propagation equation taking into account gain spectrum dynamics, gain saturation, which depends on carrier depletion, carrier heating, spectral hole-burning, group velocity dispersion, self-phase modulation and two photon absorption. Simulation of optical wave evolution in the SOA has been carried out using the finite-difference beam propagation method (FD-BPM) both in time and spectral domains. Our simulation results confirm that higher FWM conversion efficiency and lower time bandwidth product are achieved for higher absolute values of non-linear refractive index. Moreover, non-linear refractive index is more efficacious for high power propagated waves in SOAs. Finally, we have studied the modification of waveguide refractive index due to the propagation of optical pulses. We have also shown that when |n2|=1 cm2/TW, refractive index variation is in the order of 10−4 to 10−7 for high and low power input pulses, respectively.