© 2019, The Author(s). This study investigated the effects of eccentric (ECC) and concentric (CON) semi-recumbent leg cycling on global corticospinal excitability (CSE), assessed through the activity of a non-exercised hand muscle. Thirteen healthy male adults completed two 30-min bouts of moderate intensity ECC and CON recumbent cycling on separate days. Power output (POutput), heart rate (HR) and cadence were monitored during cycling. Global CSE was assessed using transcranial magnetic stimulation to elicit motor-evoked potentials (MEP) in the right first dorsal interosseous muscle before (‘Pre’), interleaved (at 10 and 20 mins, t10 and t20, respectively), immediately after (post, P0), and 30-min post exercise (P30). Participants briefly stopped pedalling (no more than 60 s) while stimulation was applied at the t10 and t20 time-points of cycling. Mean POutput, and rate of perceived exertion (RPE) did not differ between ECC and CON cycling and HR was significantly lower during ECC cycling (P = 0.01). Group mean MEP amplitudes were not significantly different between ECC and CON cycling at P0, t10, t20, and P30 and CON (at P > 0.05). Individual participant ratios of POutput and MEP amplitude showed large variability across the two modes of cycling, as did changes in slope of stimulus-response curves. These results suggest that compared to ‘Pre’ values, group mean CSE is not significantly affected by low-moderate intensity leg cycling in both modes. However, POutput and CSE show wide inter-participant variability which has implications for individual neural responses to CON and ECC cycling and rates of adaptation to a novel (ECC) mode. The study of CSE should therefore be analysed for each participant individually in relation to relevant physiological variables and account for familiarisation to semi-recumbent ECC leg cycling.