Over the last decades, conventional transcutaneous electrical nerve stimulation (TENS) has been utilized as an efficient rehabilitation intervention for alleviation of chronic pain, including phantom limb pain (PLP). However, recently the literature has increasingly focused on alternative temporal stimulation patterns such as pulse width modulation (PWM). While the effect of non-modulated high frequency (NMHF) TENS on somatosensory (SI) cortex activity and sensory perception has been studied, the possible alteration following PWM TENS at the SI has not yet been explored. Therefore, we investigated the cortical modulation by PWM TENS for the first time and conducted a comparative analysis with the conventional TENS pattern. We recorded sensory evoked potentials (SEP) from 14 healthy subjects before, immediately, and 60 min after TENS interventions (PWM and NMHF). The results revealed suppression of SEP components, theta, and alpha band power simultaneously associated with the perceived intensity reduction when the single sensory pulses applied ipsilaterally to the TENS side. The reduction of N1 amplitude, theta, and alpha band activity occurred immediately after both patterns remained at least 60 min. However, the P2 wave was suppressed right after PWM TENS, while NMHF could not induce significant reduction immediately after the intervention phase. As such, since PLP relief has been shown to be correlated with inhibition at somatosensory cortex, we, therefore, believe that the result of this study provides further evidence that PWM TENS may also be potential therapeutic intervention for PLP reduction. Future studies on PLP patients with PWM TENS sessions is needed to validate our result.