Background - Computerised cognitive behaviour therapy (cCBT) involves standardised, automated, interactive self-help programmes delivered via a computer. Randomised controlled trials (RCTs) and observational studies have shown than cCBT reduces depressive symptoms as much as face-to-face therapy and more than waiting lists or treatment as usual. cCBT’s efficacy and acceptability may be influenced by the “human” support offered as an adjunct to it, which can vary in duration and can be offered by people with different levels of training and expertise. Methods/design - This is a two-by-two factorial RCT investigating the effectiveness, cost-effectiveness and acceptability of cCBT supplemented with 12 weekly phone support sessions are either brief (5–10 min) or extended (20–30 min) and are offered by either an expert clinician or an assistant with no clinical training. Adults with non-suicidal depression in primary care can self-refer into the study by completing and posting to the research team a standardised questionnaire. Following an assessment interview, eligible referrals have access to an 8-session cCBT programme called Beating the Blues and are randomised to one of four types of support: brief-assistant, extended-assistant, brief-clinician or extended-clinician. A sample size of 35 per group (total 140) is sufficient to detect a moderate effect size with 90% power on our primary outcome measure (Work and Social Adjustment Scale); assuming a 30% attrition rate, 200 patients will be randomised. Secondary outcome measures include the Beck Depression and Anxiety Inventories and the PHQ-9 and GAD-7. Data on clinical outcomes, treatment usage and patient experiences are collected in three ways: by post via self-report questionnaires at week 0 (randomisation) and at weeks 12 and 24 post-randomisation; electronically by the cCBT system every time patients log-in; by phone during assessments, support sessions and exit interviews. Discussion - The study’s factorial design increases its efficiency by allowing the concurrent investigation of two types of adjunct support for cCBT with a single sample of participants. Difficulties in recruitment, uptake and retention of participants are anticipated because of the nature of the targeted clinical problem (depression impairs motivation) and of the studied interventions (lack of face-to-face contact because referrals, assessments, interventions and data collection are completed by phone, computer or post).