Abstract Background Major depressive disorder (MDD) is a prevalent and severe disorder. Although effective treatments for MDD are available, many patients remain untreated, mainly because of insufficient treatment capacities in the health care system. Resulting waiting periods are often associated with prolonged suffering and impairment as well as a higher risk of chronification. Web-based interventions may help to alleviate these problems. Numerous studies provided evidence for the efficacy of web-based interventions for depression. The aim of this study is to evaluate a new web-based guided self-help intervention (GET.ON-Mood Enhancer-WL) specifically developed for patients waiting to commence inpatient therapy for MDD. Methods In a two-armed randomised controlled trial ( n  = 200), the web-based guided intervention GET.ON-Mood Enhancer-WL in addition to treatment as usual (TAU) will be compared with TAU alone. The intervention contains six modules (psycho education, behavioural activation I & II, problem solving I & II, and preparation for subsequent inpatient depression therapy). The participants will be supported by an e-coach, who will provide written feedback after each module. Inclusion criteria include a diagnosis of MDD assessed with a structured clinical interview [SCID] and a waiting period of at least three weeks before start of inpatient treatment. The primary outcome is observer-rated depressive symptom severity (HRSD 24 ). Further (explorative) questions include whether remission will be achieved earlier and by more patients during inpatient therapy because of the web-based preparatory intervention. Discussion If GET.ON-Mood Enhancer-WL is proven to be effective, patients may start inpatient therapy with reduced depressive symptom severity, ideally leading to higher remission rates, shortened inpatient therapy, reduced costs, and decreased waiting times. Trial registration German Clinical Trial Registration (DRKS): DRKS00004708 .