Blood flow restriction training (BFRT) has been proposed for elderly and clinical populations with weakness. Before being used in these populations it is important to understand the neurological effects of, and subject perceptions to, BFRT. Seventeen healthy subjects were recruited and performed 2 experimental sessions, BFRT and training without blood flow restriction (TR-only), on separate days. Four sets of concentric/eccentric dorsiflexion contractions against theraband resistance were performed. Surface electromyography of the tibialis anterior was recorded during exercise and for the electrophysiological measures. At baseline, immediately-post, 10-min-post and 20-min-post exercise, motor evoked potentials (MEPs) from single pulse transcranial magnetic stimulation (TMS), paired-pulse TMS with interstimulus intervals of 2-ms (SICI) and 15-ms (ICF), and the M-max amplitude were recorded in the resting TA. Following training, subjects provided a numerical rating of the levels of pain, discomfort, fatigue, focus and difficulty during training. Muscle activation was higher in the last 20 contractions during BFRT compared to TR. There was no difference (time × condition interaction) between BFRT and TR for single-pulse MEP, SICI, ICF or M-max amplitude. There was a significant main effect of timepoint for single-pulse MEP and M-max amplitudes with both significantly reduced for 20-min-post exercise. No reductions were observed for SICI and ICF amplitudes. Taken together, BFRT and TR-only were only different during exercise and both regimes induced similar significant reductions in M-Max and MEP-amplitude post-training. Due to the lack of changes in SICI and ICF, it is unlikely that changes occurred in cortical sites related to these pathways. The increased surface electromyography activity in the last 20 contractions, indicate that the training regimes are different and that BFRT possibly induces more fatigue than TR. As such, BFRT could be used as an adjunct to conventional training. However, as subjects perceived BFRT as more painful, difficult and uncomfortable than TR-only, people should be selected carefully to undertake BFRT.