Emerging evidence suggests that regular physical activity can impact cortical function and facilitate plasticity. In the present study, we examined how physical activity levels influence corticospinal excitability and intracortical circuitry in motor cortex following a single session of moderate intensity aerobic exercise. We aimed to determine whether exercise-induced short-term plasticity differed between high versus low physically active individuals. Participants included twenty-eight young, healthy adults divided into two equal groups based on physical activity level determined by the International Physical Activity Questionnaire: low-to-moderate (LOW) and high (HIGH) physical activity. Transcranial magnetic stimulation was used to assess motor cortex excitability via motor evoked potential (MEP) recruitment curves for the first dorsal interosseous (FDI) muscle at rest (MEPREST) and during tonic contraction (MEPACTIVE), short-interval intracortical inhibition (SICI) and facilitation (SICF), and intracortical facilitation (ICF). All dependent measures were obtained in the resting FDI muscle, with the exception of AMT and MEPACTIVE recruitment curves that were obtained during tonic FDI contraction. Dependent measures were acquired before and following moderate intensity aerobic exercise (20 mins, ~60% of the age-predicted maximal heart rate) performed on a recumbent cycle ergometer. Results indicate that MEPREST recruitment curve amplitudes and area under the recruitment curve (AURC) were increased following exercise in the HIGH group only (p = 0.002 and p = 0.044, respectively). SICI and ICF were reduced following exercise irrespective of physical activity level (p = 0.007 and p = 0.04, respectively). MEPACTIVE recruitment curves and SICF were unaltered by exercise. These findings indicate that the propensity for exercise-induced plasticity is different in high versus low physically active individuals. Additionally, these data highlight that a single session of aerobic exercise can transiently reduce inhibition in the motor cortex regardless of physical activity level, potentially priming the system for plasticity induction.