Detecting neuroplastic changes during locomotor neurorehabilitation is crucial for independent primal motor behaviours. However, long-term locomotor training-related neuroplasticity remains unexplored. We compared the effects of end-effector robot-assisted gait training (E-RAGT) and bodyweight-supported treadmill training (BWST) on cortical activation in individuals with hemiparetic stroke. Twenty-three men and five women aged 53.2 ± 11.2 years were recruited and randomly assigned to participate in E-RAGT (n = 14) or BWST (n = 14) for 30 min/day, 5 days/week, for 4 weeks. Cortical activity, lower limb motor function, and gait speed were evaluated before and after training. Activation of the primary sensorimotor cortex, supplementary motor area, and premotor cortex in the affected hemisphere significantly increased only in the E-RAGT group, although there were no significant between-group differences. Clinical outcomes, including the Fugl-Meyer assessment (FMA), timed up and go test, and 10-m walk test scores, improved after training in both groups, with significantly better FMA scores in the E-RAGT group than in the BWST group. These findings suggest that E-RAGT effectively improves neuroplastic outcomes in hemiparetic stroke, although its superiority over conventional training remains unclear. This may have clinical implications and provides insight for clinicians interested in locomotor neurorehabilitation after hemiparetic stroke.Trial Registration: ClinicalTrials.gov Identifier NCT04054739 (12/08/2019).