Abstract Objectives I-wave periodicity repetitive paired-pulse transcranial magnetic stimulation (iTMS) can modify acquisition of a novel motor skill, but the associated neurophysiological effects remain unclear. The current study therefore used combined TMS-electroencephalography (TMS-EEG) to investigate the neurophysiological effects of iTMS on subsequent visuomotor training (VT). Methods Sixteen young adults (26.1 ± 5.1 years) participated in three sessions including real iTMS and VT (iTMS + VT), control iTMS and VT (iTMS sham + VT), or iTMS alone. Motor-evoked potentials (MEPs) and TMS-evoked potentials (TEPs) were measured before and after iTMS, and again after VT, to assess neuroplastic changes. Results Irrespective of the intervention, MEP amplitude was not changed after iTMS or VT ( P = 0.211). Motor skill was improved compared with baseline ( P < 0.001), but no differences were found between stimulus conditions. In contrast, the P30 peak was altered by VT when preceded by sham iTMS ( P < 0.05), but this effect was not apparent when VT was preceded by iTMS or following iTMS alone (all P > 0.15). Conclusion In contrast to expectations, iTMS was unable to modulate MEP amplitude or influence motor learning. Despite this, changes in P30 amplitude suggested that motor learning was associated with altered cortical reactivity. Furthermore, this effect was abolished by priming with iTMS, suggesting an influence of priming that failed to impact learning. Authorship statements Conceptualization: JGS; Data curation: RS, BJH, and WL; Formal analysis: RS; Funding acquisition: RS; Investigation: RS, BJH, and WL; Methodology: RS, GMO, BJH and JGS; Project administration: GMO and JGS; Supervision: GMO and JGS; Roles/Writing - original draft: RS and GMO; Writing - review & editing: BJH, WL, and JGS.