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Abstract Background Major depression is a highly prevalent disorder causing severe personal distress, and high societal costs. Patients with depression often have comorbid insomnia disorder (ID) leading to even worse personal distress and worse treatment outcomes. Recent results from a non-randomised pilot study with internet-delivered Cognitive Behavioural Therapy (CBTi) for Insomnia (I-Sleep) added to regular depression care were promising regarding feasibility and initial effects on insomnia complaints and depression. However, no randomised controlled trial (RCT) has been performed yet to access the (cost-) effectiveness of I-Sleep for depression. Therefore, this protocol article presents the design of an RCT aimed to assess the (cost-) effectiveness of I-Sleep in addition to usual care for depression compared to usual care alone in depressed patients with a comorbid Insomnia Disorder (ID) treated at outpatient clinics for mood disorders. Methods /design This is a multi-centre RCT with measurements at baseline and at 3, 6, 9, and 12 months of follow-up. Patients with depression and an ID are randomised to either I-Sleep treatment followed by regular depression care or to regular depression care alone. Our aim is to recruit one hundred and seventy-five patients from multiple outpatient clinics for mood disorders. The primary outcome is the change in depressive symptoms over 12 months of follow-up measured with the Patient Health Questionnaire (PHQ-9). Secondary outcomes are recovery from depression (PHQ-9), insomnia severity (Insomnia Severity Index, ISI), daily functioning (Work and Social Adjustment Scale, WSAS), general quality of life (EuroQol 5-level version, EQ-5D-5L), and societal costs (Adapted versions of the iMTA Productivity Cost Questionnaire, iPCQ and iMTA Medical Cost Questionnaire, iMCQ). Discussion We hypothesize that the addition of I-Sleep to usual care will result in a significant improvement in depression treatment outcomes and quality of life as well as a decrease in healthcare and societal costs compared to usual care alone. This study is the first pragmatic RCT evaluating the effectiveness and cost-effectiveness of adding CBTi to usual care for depression. Trial registration Netherlands Trial Register (NL8955). Registered on October 6th2020. https://trialsearch.who.int/Trial2.aspx?TrialID=NL8955