Among substances, opiates and psychostimulants are responsible for the most significant public health problems, yet few studies have characterized their similarities or differences in the cortical plasticity of individuals with these substance related problems. This investigation utilized concurrent transcranial magnetic stimulation and electroencephalography (TMS-EEG) to examine cortical plasticity characteristics of individuals with heroin and methamphetamine related substance use disorder (SUD) relative to healthy controls. TMS-EEG data were collected from healthy control subjects ( = 35), subjects with heroin ( = 72) and methamphetamine ( = 69) use disorder. The data were analyzed using our fully-automated artifact rejection algorithm (ARTIST). Analyses were performed separately for F3, F4 and P3 stimulation sites. Linear mixed effects models were used to examine Group (heroin, methamphetamine, healthy control) x Time (pre, post single-session rTMS) interactions. To evaluate plasticity differences across groups, we observed the changes in single pulse TMS before and after single-session of rTMS. There was no change in alpha power after stimulation of the F3 or F4 sites across groups. The alpha power of the control group was significantly decreased when stimulating the P3 site, while there was no significant change in alpha power for either drug group during the same time window. The beta power of the healthy control group increased significantly when the F3 site was stimulated. In contrast, there was no significant change in either the methamphetamine or heroin group. Following a single-session of rTMS intervention, there was a significant difference in alpha-band power between the healthy control group and the two drug groups. Taking together, the study findings identified differential plasticity effects in the two types of SUD population, and highlighted the network effects of rTMS. The findings point to an exciting future path for using rTMS to test new plasticity-based interventions for treating drug addiction.