The high prevalence and severe consequences of poor sleep following acquired brain injury emphasises the need for an effective treatment. However, treatment studies are scarce. The present study evaluates the efficacy of blended online cognitive behavioural therapy for insomnia (eCBT-I) developed specifically for people with acquired brain injury. In a multicentre prospective, open-label, blinded end-point randomised clinical trial, 52 participants with insomnia and a history of a stroke or traumatic brain injury were randomised to 6 weeks of guided eCBT-I or treatment as usual, with a 6-week follow-up. The primary outcome measure was the change in insomnia severity between baseline and after treatment, measured with the Insomnia Severity Index. Results showed that insomnia severity improved significantly more with eCBT-I than with treatment as usual compared to baseline, both at post-treatment (mean [SEM] 4.0 [1.3] insomnia severity index points stronger decrease, d = 0.96, p < 0.003) and at follow-up (mean [SEM] 3.2 [1.5] insomnia severity index points, d = −0.78, p < 0.03). In conclusion, our randomised clinical trial shows that blended CBT is an effective treatment for insomnia, and feasible for people with acquired brain injury, regardless of cognitive and psychiatric complaints. Online treatment has major advantages in terms of availability and cost and may contribute to the successful implementation of insomnia treatment for people with acquired brain injuries.