BackgroundGerman statutory health insurances are pursuing the goal of improving treatment of chronically ill people by promoting networks of health care providers and supporting treatments that reflect the current medical knowledge. The so-called PNP program is a collaborative care program developed by a German statutory health insurance, which defines specific rules on psychiatric, neurological, psychosomatic, and psychotherapeutic treatment. It aims to strengthen provision of guideline-based outpatient treatment and collaboration between different health care providers. It includes the general practitioners’ program, which aims to strengthen the coordinating role of GPs. This study aims to evaluate the PNP program.MethodsTo evaluate the effectiveness of the PNP program, we will conduct a prospective non-randomized controlled trial with primary data comparing patients enrolled in the PNP program and in the general practitioner program (intervention group) to patients enrolled only in the general practitioner program and patients who receive usual care (control groups). To evaluate costs and level of detail of diagnoses in care of patients with PNP program, we will use routinely collected secondary administrative health data in a retrospective quasi-experimental design. Patients who are at least 18 years old, insured by the statutory health insurance AOK, and on sick leave due to one of the mental or neurological diagnoses (affective, anxiety, somatoform or adjustment disorders, alcohol use disorders, schizophrenia, multiple sclerosis) will be included. We will collect data at baseline and at 12-months follow-up. Health-related quality of life (primary data) and direct costs (secondary data) caused by outpatient and inpatient service utilization and medication will be the primary outcomes. We will analyze data using (generalized) linear mixed models and exploratory analyses. We will use entropy balancing to control for possible differences between the groups. We will use an exploratory sequential design including qualitative and descriptive statistical analyses to assess the structure and process quality of the PNP program among health care providers.DiscussionThe results will help to develop a comprehensive picture of collaborative care programs for mental and neurological health care from the perspective of patients, health care providers, and health insurance companies.Trial registrationGerman Clinical Trial Register DRKS00013114Electronic supplementary materialThe online version of this article (10.1186/s12888-018-1914-5) contains supplementary material, which is available to authorized users.