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Repetitive and alternating lower limb movements are a specific component of human gait. Due to technical challenges, the neural mechanisms underlying such movements have not been previously studied with functional magnetic resonance imaging. In this study, we present a novel treadmill device employed to investigate the kinematics and the brain activation patterns involved in alternating and repetitive movements of the lower limbs. Once inside the scanner, 19 healthy subjects were guided by two visual cues and instructed to perform a motor task which involved repetitive and alternating movements of both lower limbs while selecting their individual comfortable amplitude on the treadmill. The device facilitated the performance of coordinated stepping while registering the concurrent lower-limb displacements, which allowed us to quantify some movement primary kinematic features such as amplitude and frequency. During stepping, significant blood oxygen level dependent signal increases were observed bilaterally in primary and secondary sensorimotor cortex, the supplementary motor area, premotor cortex, prefrontal cortex, superior and inferior parietal lobules, putamen and cerebellum, regions that are known to be involved in lower limb motor control. Brain activations related to individual adjustments during motor performance were identified in a right lateralized network including striatal, extrastriatal, and fronto-parietal areas.