Functional MRI studies on patients with multiple sclerosis (MS) have demonstrated widespread cortical reorganization of the motor network. However, few functional studies have addressed cortical plasticity in patients with clinically isolated syndrome (CIS). The activity of the lower limb motor system, despite its highlighted involvement in patients with CIS and MS, has been little studied. Thus, brain activation was compared in CIS patients with clinically intact motor systems with that in healthy control participants while they were performing motor tasks with four limbs. A total of 26 right-handed patients with CIS with clinically intact motor systems and 28 right-handed age and sex-matched controls participated in the functional MRI (fMRI) motor task. Patients with CIS showed greater activation in the ipsilateral secondary somatosensory cortex, cingulate gyrus and precuneus cortex while performing the ankle movement task compared to healthy controls. In the finger-tapping task, patients with CIS showed greater activity in the contralateral thalamus, ipsilateral premotor and superior temporal gyrus. In addition, the left inferior frontal gyrus was activated more in patients with CIS, regardless of the hand used. Therefore, despite having clinically intact motor systems, patients with CIS had different motor networks. All novel recruited regions were adjacent to the somatotopy of the primary motor areas of the limbs. Our finding confirm that brain reorganization precedes clinical manifestation, as no patient had any clinical manifestation that suggested involvement of the motor system.