Abstract Background Phobic disorders are highly prevalent and constitute a considerable burden for patients and society. As patients wait for face-to-face psychotherapy for phobic disorders in outpatient clinics, this time can be used for guided self-help interventions. The aim of this study is to investigate a five week internet-based guided self-help programme of exposure therapy in terms of clinical effectiveness and impact on speed of recovery in psychiatric outpatients, as well as the cost-effectiveness of this pre-treatment waiting list intervention. Methods/design A randomised controlled trial will be conducted among 244 Dutch adult patients recruited from waiting lists of outpatient clinics for face-to-face psychotherapy for phobic disorders. Patients suffering from at least one DSM-IV classified phobic disorder (social phobia, agoraphobia or specific phobia) are randomly allocated (at a 1:1 ratio) to either a five-week internet-based guided self-help program followed by face-to-face psychotherapy, or a control group followed by face-to-face psychotherapy. Waiting list status and duration are unchanged and actual need for further treatment is evaluated prior to face-to-face psychotherapy. Clinical and economic self-assessment measurements take place at baseline, post-test (five weeks after baseline) and at 3, 6, 9 and 12 months after baseline. Discussion Offering pre-treatment internet-based guided self-help efficiently uses time otherwise lost on a waiting list and may increase patient satisfaction. Patients are expected to need fewer face-to-face sessions, reducing total treatment cost and increasing speed of recovery. Internet-delivered treatment for phobias may be a valuable addition to psychotherapy as demand for outpatient treatment increases while budgets decrease. Trial registration Netherlands Trial Register NTR2233