A differential equation governing the wakefield potential (φ) in a plasma filled rectangular waveguide is derived analytically. This equation is solved numerically for the wakefield (Ew) generated with the help of three kinds of microwave pulses, namely sine pulse (SP), rectangular Gaussian pulse (RGP), and rectangular triangular pulse (RTP). The effect of microwave frequency (f), pulse duration (τ), waveguide width (b), equilibrium plasma density (n0), and microwave intensity (I) on the amplitude of the wakefield is studied. This amplitude is increased for the longer pulse duration and higher microwave intensity, but is decreased with growing waveguide width for all types of pulses. With regard to the variation of wakefield amplitude with plasma density, the RTP and SP behave in a similar fashion and the RGP behaves oppositely. The amplitude for the case of RGP gets increased with the plasma density. The amplitude is enhanced at larger microwave frequency for the cases of RGP and SP, but is decreased for the case of RTP. The comparative study of three types of pulses shows that the wakefield with larger amplitude is achieved with the help of rectangular triangular pulse, which is found to be sensitive with waveguide width, pulse duration and microwave intensity.