Transcranial magnetic stimulation (TMS) is a form of non-invasive brain stimulation commonly used to modulate neural activity. Despite three decades of examination, the generation of flexible magnetic pulses is still a challenging technical question. It has been revealed that the characteristics of pulses influence the bio-physiology of neuromodulation. In this study, a second-generation programmable TMS (xTMS) equipment with advanced stimulus shaping is introduced that uses cascaded H-bridge inverters and a phase-shifted pulse-width modulation (PWM). A low-pass RC filter model is used to estimate stimulated neural behavior, which helps to design the magnetic pulse generator, according to neural dynamics. The proposed device can generate highly adjustable magnetic pulses, in terms of waveform, polarity and pattern. We present experimental measurements of different stimuli waveforms, such as monophasic, biphasic and polyphasic shapes with peak coil current and the delivered energy of up to 6 kA and 250 J, respectively. The modular and scalable design idea presented here is a potential solution for generating arbitrary and highly customizable magnetic pulses and transferring repetitive paradigms.