In this study, the neural response to pulse-width modulated (PWM) transcranial magnetic stimulation (TMS) is estimated using a computational neural model which simulates the response of cortical neurons to TMS. The recently introduced programmable TMS uses PWM to approximate conventional resonance-based TMS pulses by fast switching between voltage levels. The effect of such stimulation on the six cortical layers is modelled by estimating the activation threshold of the neurons. Modelling results are compared between the novel device and that of conventional TMS stimuli generated by Magstim stimulators. The neural responses to the PWM pulses and the conventional stimuli show a high correlation, which validates the use of pulse-width modulated pulses in TMS.Clinical Relevance- This computational modelling study demonstrates an equivalent effect of PWM and conventional TMS pulses on the nervous system which paves the way to more flexibility in exploring and choosing stimulation parameters for TMS treatment.