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Neurocognitive disturbance with subjectively-impaired concentration and memory is a common, disabling symptom reported by patients with chronic fatigue syndrome (CFS). We recently reported preliminary evidence for benefits of cognitive remediation as part of an integrated cognitive-behavioral therapy (CBT)/ graded exercise therapy (GET) program. Here, we describe a contemporaneous, case-control trial evaluating the effectiveness of an online cognitive remediation training program (cognitive exercise therapy; CET) in addition to CBT/GET (n=36), compared to CBT/GET alone (n=36). The study was conducted in an academic, tertiary referral outpatient setting over 12 weeks (11 visits) with structured, home-based activities between visits. Participants self-reported standardized measures of symptom severity and functional status before and after the intervention. Those in the CET arm also completed standardized neurocognitive assessment before, and following, treatment. The addition of formal CET led to significantly greater improvements in self-reported neurocognitive symptoms compared to CBT/GET alone. Subjective improvement was predicted by CET group and lower baseline mood disturbance. In the CET group, significant improvements in objectively-measured executive function, processing speed, and working memory were observed. These subjective and objective performance improvements suggest that a computerized, home-based cognitive training program may be an effective intervention for patients with CFS, warranting randomized controlled trials.