Persistent post concussion symptoms (PPCS) describe the condition when an individual experiences chronic symptoms, particularly fatigue, beyond the expected time of recovery. The aim of this study was to quantify the effect of fatigue and related ongoing symptoms on somatosensory and corticomotor pathways using reaction time (RT) testing, and single-pulse and paired-pulse transcranial magnetic stimulation (TMS). Eighty-three participants (nine female, mean age 37.9 ± 11.5 years) were divided into two groups (persistent symptoms versus asymptomatic) following self-report based upon previously published clinical symptom scores. All participants completed somatosensory and visuomotor RT testing, as well as corticomotor excitability and inhibition measurements via TMS. Participants in the persistent symptom group (n = 38) reported greater number of previous concussions (t = 2.81, p = 0.006) and significantly higher levels of fatigue and related symptoms in the asymptomatic group (n = 45; t = 11.32, p < 0.006). Somatosensory RT showed significant slowing and increased variability in the persistent symptoms group (p < 0.001), however no significant differences were observed between groups for visuomotor RTs. Transcranial magnetic stimulation revealed differences between groups for intracortical inhibition at all stimulus intensities and paired pulse measures. The results indicate that somatosensory and corticomotor systems reflect on-going fatigue. From a practical perspective, objective and simplistic measures such as somatosensory and corticomotor measures can be used in the assessment of PPCS and gauging the efficacy of post concussion rehabilitation programmes.