BACKGROUND Depressive and anxiety disorders are highly prevalent, but only a small percentage (approximately 50%) of patients receive appropriate treatment. Relevant barriers include communication and coordination gaps between different providers that result from the lack of integration between different care-giving systems. Aftercare following inpatient treatment represents one of these gaps because systematic follow-up care does not exist. Case management-based aftercare coordination by phone might be a promising approach to overcoming this gap and improving long-term treatment outcomes. Case management is a patient-centered and situation-based approach comprising systematic tracking and support of patients by a case manager. The aim of this study is to evaluate the effectiveness of aftercare coordination by phone for patients with depressive and anxiety disorders. METHODS/DESIGN The effectiveness of aftercare coordination will be investigated in a prospective randomized controlled trial in four psychotherapeutic inpatient routine care units (St. Franziska-Stift Bad Kreuznach, MediClin Seepark Klinik Bad Bodenteich, Segeberger Kliniken Gruppe Bad Segeberg and Luisenklinik Bad Dürrheim). The patients receiving aftercare coordination (intervention group; IG) will be compared with those who receive treatment as usual (TAU control group; CG). Eligible patients will be required to have a diagnosis of an anxiety and/or depressive disorder and a recommendation for follow-up outpatient psychotherapy. The aftercare coordination consists of six phone contacts at intervals of two weeks that are performed by therapists in the inpatient units. The patients will complete questionnaires at discharge (t1), 3 months after discharge (i.e., at the end of the intervention (t2)) and 9 months after discharge (t3). The primary outcome will be change in symptom severity from t1 to t3, the secondary outcomes will be health-related quality of life and the proportion of patients who manage to begin outpatient psychotherapy by t3. DISCUSSION This study will determine whether case management-based aftercare coordination by phone is an adequate approach for overcoming treatment barriers in the clinical pathways of patients with depressive and anxiety disorders. If proven effective, an accessible supplementary treatment approach that will help to maintain and even improve long-term treatment outcomes will be made available for patients following inpatient treatment.