<i>Background:</i> Estimates of the prevalence of cognitive impairment among patients with multiple sclerosis (MS) range between 40 and 70%. The current cerebral functional system (CFS) of the Expanded Disability Status Scale (EDSS) is subjective. <i>Aim:</i> To define a new cerebral functional system (NCFS) based on neuropsychological evaluation (NE). <i>Methods:</i> We prospectively included 215 MS patients. NE evaluated cognitive functions. Fatigue was assessed with the Fatigue Impact Scale. The NCFS was devised with grades from 0 to 5, excluding depression but including fatigue. Grade 1 of the NCFS was integrated in the EDSS as other functional scores. The NCFS and new EDSS including the NCFS were compared with the current CFS and EDSS. <i>Results:</i> 215 patients (69% women, 67% with relapsing-remitting MS, median EDSS 3.0) were assessed. 98% of these patients presented fatigue and/or cognitive impairment with the NCFS compared to 62% with the CFS. The NCFS was higher than the CFS, and the EDSS had changed in 31% of the 113 patients with an EDSS <3.5. Change in functional score was not correlated to current age or age at onset of MS. <i>Conclusions:</i> We propose a new CFS grading based on NE, including fatigue, and integrating grade 1 at EDSS.