Purpose: Fibromyalgia syndrome (FMS) and rheumatoid arthritis (RA) are chronic pain disorders, with clearly distinct pathogenetic mechanisms, frequently accompanied by symptoms like depression, fatigue, insomnia and cognitive problems. This study compared performance in various cognitive domains between patients with FMS and RA. The role of clinical symptoms severity in determine the differences in cognitive performance was also investigated. Patients and Methods: A cross-sectional study was conducted according to the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) Statement. In total, 64 FMS patients, 34 RA patients and 32 healthy controls participated, all women. Using factor analysis, questionnaire scores were combined to yield a symptom severity factor, which was used as a control variable in the group comparisons. Results: Without controlling for symptom severity, both patient groups performed worse than controls in all the cognitive domains assessed (visuospatial memory; verbal memory; strategic planning and self-regulation; processing speed, attention and cognitive flexibility; and planning and organizational abilities); overall deficits were greater in FMS than in RA patients. FMS patients reported more severe clinical symptoms (current pain intensity, total pain, state anxiety, depression, fatigue and insomnia) than RA patients. After controlling for symptom severity, a large proportion of the cognitive test parameters no longer differed between FMS and RA patients. Conclusion: The study confirmed significant impairments in attention, memory, and higher cognitive functions in both FMS and RA. The greater deficits seen in FMS patients may at least partly be explained by more severe pain and secondary symptoms. Cognitive screening may facilitate the development of personalized treatment plans to optimize the quality of life of FMS and RA patients.