Background: Up to a third of stroke patients and patients with traumatic brain injury suffer from insomnia, including problems to fall asleep or stay asleep at night. Insomnia may exacerbate other brain damage-related problems, for example regarding cognitive functioning and emotional well-being; may lead to poorer quality of life; and may complicate recovery processes. Cognitive behavioral therapy for insomnia, delivered face-to-face or online, is found to be effective in the general population. However, despite the high prevalence and serious consequences of insomnia following acquired brain injury, studies on the efficacy of face-to-face cognitive behavioral treatment in this population are scarce, and this applies even more for studies on online cognitive behavioral therapy. Therefore, this study aims to evaluate the efficacy of a newly developed guided online cognitive behavioral therapy for insomnia following acquired brain injury. Methods: A multicenter, prospective, randomized, open-label, blinded end point study (PROBE) will be conducted, in which 48 patients diagnosed with stroke or traumatic brain injury and insomnia will be randomly allocated to the online cognitive behavioral therapy for insomnia treatment group or the treatment as usual group. The treatment consists of 6 online cognitive behavioral therapy sessions given on a weekly basis and personalized feedback after each session, combined with 2 face-to-face sessions. Outcomes will be assessed at baseline, immediately after the intervention period and at 6-week follow-up. The primary outcome is the insomnia severity assessed with the Insomnia Severity Index. Secondary outcome measures include sleep quality, sleep features derived from the sleep diary, fatigue, anxiety and depression, subjective cognitive functioning, and societal participation. Discussion: This study will provide insight on the efficacy of online cognitive behavioral therapy for insomnia following stroke and traumatic brain injury. Trial registration: Netherlands Trial Register NTR7082. Registered on 12 March 2018.