Pulsed power systems often use a pulse transformer to generate high voltage pulses in some application such as radar systems, linear accelerators, and klystron modulators. Parasitic parameters include leakage inductance and capacitances are crucial for output waveform of pulse transformers. To ensure a rectangular pulse shape with a fast rise time, a required small overshoot and an acceptable voltage droop, theoretical calculation based on MATLAB is studied to optimize the design of the pulse transformer in this paper. Based on the theoretical calculation results, Finite Element Method simulations of magnetic and electric fields are carried out to obtain a more precise model for designing the transformer. Additionally, as the pulse transformer related in this paper works on the single forward state, a dc reset circuit, which can improve the utilization of the core material is implemented. Finally, accurate simulations of the pulse system equivalent circuit based on SABER are implemented. Meanwhile, output waveforms of pulse systems with different parasitic parameters and variable load are discussed. The simulation and experiment results showed that the optimum design of pulse transformer based on MATLAB programming and SABER simulation is effective to reduce the rise time of rectangular pulse shape to 1.5 μs while the pulse duration is as large as 200 μs.