Joubert syndrome (JS) is a rare genetic disorder characterized by a congenital malformation of the hindbrain, and accompanied by axonal decussation abnormalities affecting the corticospinal tract and the superior cerebellar peduncles. To the best of our knowledge, there are no reports of normal pyramidal decussation in JS. Here, we describe the case of an 18-year-old boy presenting midline-crossing corticospinal projections, which were considered normal corticospinal tract trajectories. Diffusion tensor imaging and motor evoked potential study analysis demonstrated the exclusive presence of decussating corticospinal projections in the patient. Based on these results, we suggest that JS might be associated with several, diverse corticospinal motor tract organization patterns.