In this paper, we have calculated the band structure of strained quantum well (QW) semiconductor optical amplifiers (SOAs) by using plane wave expansion method (PWEM) and finite difference method (FDM), respectively. The difference between these two numerical methods is presented. First, the solution of Schr?dinger’s equation in a conduction band for parabolic potential well is used to check the validity and accuracy of these two numerical methods. For the PWEM, its stability and computational speed are investigated as a function of the number of plane waves and the period of QW. For FDM, effects of mesh size and QW width on its accuracy and calculation time are discussed. Finally, we find that the computational speed of FDM generally is faster than that of PWEM. However, the PWEM is more efficient than the FDM when wider SOAs are needed to be calculated. Therefore, to obtain high accuracy and efficient numerical solutions for band structures, numerical methods should be selected depending on required accuracy, device structure and further applications.