Fibromyalgia (FMS) is a chronic condition that encompasses widespread pain associated with cognitive impairment and significant emotional distress related to functional disability. This study aimed to obtain evidence of the role of pain in the effect of time since FMS diagnosis and cognitive performance using a novel online protocol of neuropsychological evaluation since the COVID-19 pandemic has challenged traditional neuropsychology testing leading to the need for novel procedures transitioning to tele-neuropsychology. A sample of 70 adult women was evaluated (50 with FMS and 19 controls) using online questionnaires that evaluated pain and executive functioning (impulsivity, inhibition control, monitoring, and planning). Afterward, participants were evaluated by trained neuropsychologists in a 30 min online session using virtually adapted cognitive tests: the Hopkins Verbal Learning Test (memory), the Symbol-Digit Modalities Test (attention and speed processing), the F-A-S test (verbal fluency), and Digit Span tests (working memory). We found that the time of FMS diagnosis has an effect on cognitive functioning predominantly mediated by pain. Our results point out the role of pain as a mediator on cognitive performance, specifically in executive functions which are directly affected by the cumulative effect of the time of diagnosis. Furthermore, the importance of considering a broader perspective for assessment and treatment including novel procedures via tele-neuropsychology.