Abstract Fibromyalgia (FMS) is a chronic condition that encompasses widespread pain associated with cognitive impairment and significant emotional distress related to functional disability that affects mainly women. However, the mechanisms underlying the origin of the cognitive impairments and how the current COVID-19 pandemic impacts remain elusive. This study aimed to determine whether there is an association between cognitive performance in executive functions, physical pain, and psychological distress caused by the pandemic in a group of Chilean women with FMS using a novel online protocol of neuropsychological evaluation. We found that women with FMS present cognitive impairment predominantly explained by pain and anxiety symptoms, which are associated with the difficulties experienced from the COVID-19 pandemic. These results point out the importance of considering a broader perspective for treatment, including anxiety symptoms and the psychological distress caused by the pandemic as a therapeutic target for cognitive impairments.