Local administration of botulinum neurotoxin type A (BoNT-A) is becoming the preferred treatment for focal spasticity, a movement disorder commonly occurring in multiple sclerosis (MS). In this study, 4 out of 10 enrolled MS patients with leg spasticity and 5 healthy controls (HCs) were included. In the patient group, the fMRI examination was performed three times: before the BoNT-A administration and at the week 4 and week 12 visits after injection. During all the examinations, subjects performed blocks of repeated knee extension-flexion alternating with rest blocks, each 15 seconds long. The patient group mean images at the week 0 examination showed significant compensatory spatial enlargement of bilateral frontoparietal sensorimotor cortices when compared to controls, whereas the results of the second examination showed significant contraction of previously activated areas with no significant difference from HCs. At the final examination, the activation areas expanded back close to their original volume, in association with the disappearance of the BoNT-A effect on spasticity. Conclusion: We conclude that motor cortex engagement reflects the BoNT-A treatment- related changes in the periphery, likely indirectly mediated by altered afferentation. This is a novel observation, although consistent with the conclusions of other studies using different methods and paradigms.