Introduction Approximately 50% of individuals with fibromyalgia (a chronic widespread pain condition) have comorbid insomnia. Treatment for these comorbid cases typically target pain, but growing research supports direct interventions for insomnia (eg, cognitive behavioural treatment for insomnia (CBT-I)) in these patients. Previous research suggests sustained hyperarousal mediated by a neural central sensitisation mechanism may underlie insomnia and chronic pain symptoms in fibromyalgia. We hypothesise CBT-I will improve insomnia symptoms, improve clinical pain and reduce central sensitisation. The trial will be the first to evaluate the short-term and long-term neural mechanisms underlying insomnia and pain improvements in fibromyalgia. Knowledge obtained from this trial might allow us to develop new or modify current treatments to better target pain mechanisms, perhaps reversing chronic pain or preventing it. Methods and analysis Female participants (n=130) 18 years of age and older with comorbid fibromyalgia (with pain severity of at least 50/100) and insomnia will be recruited from the University of Missouri in Columbia, Missouri, and surrounding areas. Participants will be randomised to 8 weeks (plus 4 bimonthly booster sessions) of CBT-I or a sleep hygiene control group (SH). Participants will be assessed at baseline, post-treatment, 6 and 12 months follow-ups. The following assessments will be completed: 2 weeks of daily diaries measuring sleep and pain, daily actigraphy, insomnia severity index, pain-related disability, single night of polysomnography recording, arousal (heart rate variability, cognitive affective arousal), structural and functional MRI to examine pain-related neural activity and plasticity and mood (depression, anxiety). Ethics and dissemination Ethics approval was obtained in July 2018 from the University of Missouri. All data are expected to be collected by 2022. Full trial results are planned to be published by 2024. Secondary analyses of baseline data will be subsequently published. Trial registration number NCT03744156 .