Background Multiple sclerosis (MS) patients commonly suffer from fatigue and define it as one of their most disabling symptom profoundly disrupting their lives. However, the relationship of fatigue to cognitive functions and its impact on quality of life have not been widely studied. Aim To define (1) “cognitive fatigue”, (2) survey its frequency and (3) characterize severity and impact on quality of life in MS patients in the first 10 years of the disease. Methods A two-wave design was utilized to enrich the studied population in subjects whose fatigue is significant. In the first wave, fatigue was measured by the self-reported fatigue severity scale (FSS) in randomly selected MS patients from our computerized database. Patients responding to the 9th item of the FSS i.e., “Fatigue interferes with my work, family, or social life” by a grade of 3 or higher (of 7) were further assessed (wave two) by the fatigue impact scale (FIS) and the RAYS quality of life questionnaire. Results Of the 259 patients that completed the first-wave screening, 158 patients (61%, 118 females, mean age 41.1 ± 9.2 years, mean disease duration 6.2 ± 5.5 years) satisfied the additional criterion and were defined to suffer from significant fatigue. The great majority of these patients–91.7%–had a relapsing–remitting disease course, mean FIS score was 77 ± 25.9 and their mean EDSS was 2.9 ± 2.6. Fatigue was reported to occur most of the day in 30.9% of patients, persist in 69% for more than 1 year, and in 59.8%, it was reported not to be associated with effort. No correlations were found between age, gender, disease duration or neurological disability and FIS cognitive subscale score. Significant correlations were found between the FIS cognitive subscale score and the three domains (physical, psychological and social-familial) of the RAYS quality of life questionnaire ( p < 0.001). Conclusions Cognitive fatigue was found in more than half of MS patients in the first decade from onset that were particularly selected for significant fatigue in their lives. This aspect of fatigue correlated with all quality of life domains and especially with psychological everyday tasks.