The simulation of light waves propagating in fibers oppositely has to handle the extremely huge volume of data when employing sequential and unidirectional methods, where the simulation is in a coordinate system that moves along with the light waves. Therefore, alternative simulation algorithm should be used when calculating counter propagating light waves. Parallelizable and bidirectional (PB) algorithm simulates the light waves matching in time domain instead of space domain, does not need iteration, and permits efficient parallelization on multiple processors. The PB method is proposed to calculate the propagation of dispersing Gaussian pulse and a bit stream in fibers. However, PB method also has apparent advantages when simulating pulses in fiber laser amplifiers, which has not been investigated detailed yet. In this paper, we perform the simulation of pulses in a rare-earth-ions doped fiber amplifier. The influence of pump power, signal power, repetition rate, pulse width and fiber length on the amplifier’s output average power, peak power, pulse energy and pulse shape are investigated. The results indicate that the PB method is effective when simulating high power amplification of pulses in fiber amplifier. Furthermore, nonlinear effects can be added into the simulation conveniently. The work in this paper will provide a more economic and efficient method to simulate power amplification of fiber lasers.