Abstract In clinical routine, it might be difficult to distinguish between fatigue and depression in Multiple sclerosis (MS). We investigated in two independent observational cohort studies which clinical and paraclinical features distinguish patients reporting fatigue but no depressive symptoms from those suffering from depressive symptoms but having no relevant fatigue. In Study 1, n = 156 MS patients underwent fatigue, depression, cognitive screening and flow cytometry measurements. In Study 2, n = 54 MS patients performed a comprehensive neuropsychological evaluation. Patients reporting predominantly fatigue symptoms were older, had a lower information processing speed and higher EDSS compared to those scoring high on depression. CD3 + CD4 + T-helper cells count distinguished patients with depressive symptoms from those with neither depression nor fatigue. Study 2 demonstrated similar results. Additionally, progressive MS was associated with fatigue. From the whole neuropsychological test battery only SDMT distinguished fatigue from depressive phenotypes with the latter performing better. In both studies the groups did not differ regarding any other baseline variable including disease activity. Older age, slow information processing, worse physical disability and progressive disease course are distinguishing features of patients reporting more fatigue than depressive symptoms. Higher peripheral inflammatory cell counts seem to characterize depression.