Training of specific muscles causes plastic changes in corticomotor pathways which may underlie the effect of various clinical rehabilitation procedures. The paired pulse transcranial magnetic stimulation (ppTMS) technique can be used to assess short interval intra-cortical inhibitory (SICI) and intra-cortical facilitatory (ICF) networks. This study examined changes in SICI and ICF in tongue motor cortex after tongue training in 11 healthy volunteers using ppTMS. Paired pulse TMS was applied to the 'hot-spot' for the tongue motor cortex and motor-evoked potentials (MEPs) were recorded from tongue muscles. In tongue motor cortex, bilateral SICI (P < 0.019) and ICF (P < 0.001) was detected before and after training. There were no significant effects of training on single MEPs or SICI/ICF (P > 0.063). The success rate improved during training (P < 0.001) and changes in success were correlated to changes in single MEP amplitude (P < 0.006) but not to SICI/ICF (P > 0.113). This first study of SICI/ICF after tongue training showed no training-related changes in intra-cortical inhibitory or facilitatory networks. However, there was an association between task performance and changes in corticomotor excitability. Further studies are required to determine the clinical utility of muscle specific training for oral rehabilitation purposes.