Abstract Background Insomnia is a highly prevalent disorder causing clinically significant distress and impairment. Furthermore, insomnia is associated with high societal and individual costs. Although cognitive behavioural treatment for insomnia (CBT-I) is the preferred treatment, it is not used often. Offering CBT-I in an online format may increase access. Many studies have shown that online CBT for insomnia is effective. However, these studies have all been performed in general population samples recruited through media. This protocol article presents the design of a study aimed at establishing feasibility, effectiveness and cost-effectiveness of a guided online intervention (i-Sleep) for patients suffering from insomnia that seek help from their general practitioner as compared to care-as-usual. Methods/design In a pragmatic randomized controlled trial, adult patients with insomnia disorder recruited through general practices are randomized to a 5-session guided online treatment, which is called “i-Sleep”, or to care-as-usual. Patients in the care-as-usual condition will be offered i-Sleep 6 months after inclusion. An ancillary clinician, known as the psychological well-being practitioner who works in the GP practice (PWP; in Dutch: POH-GGZ), will offer online support after every session. Our aim is to recruit one hundred and sixty patients. Questionnaires, a sleep diary and wrist actigraphy will be administered at baseline, post intervention (at 8 weeks), and at 6 months and 12 months follow-up. Effectiveness will be established using insomnia severity as the main outcome. Cost-effectiveness and cost-utility (using costs per quality adjusted life year (QALY) as outcome) will be conducted from a societal perspective. Secondary measures are: sleep diary, daytime consequences, fatigue, work and social adjustment, anxiety, alcohol use, depression and quality of life. Discussion The results of this trial will help establish whether online CBT-I is (cost-) effective and feasible in general practice as compared to care-as-usual. If it is, then quality of care might be increased because implementation of i-Sleep makes it easier to adhere to insomnia guidelines. Strengths and limitations are discussed. Trial registration Netherlands Trial register NTR 5202 (registered April 17 st .