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Background Integrating mental health providers into primary care clinics improves access to and outcomes of mental health care. In the Veterans Health Administration (VA) Primary Care Mental Health Integration (PCMHI) program, mental health providers are co-located in primary care clinics, but the implementation of this model is challenging outside large VA medical centers, especially for rural clinics without full mental health staffing. Long wait times for mental health care, little collaboration between mental health and primary care providers, and sub-optimal outcomes for rural veterans could result. Telehealth could be used to provide PCMHI to rural clinics; however, the clinical effectiveness of the tele-PCMHI model has not been tested. Based on evidence that implementation facilitation is an effective implementation strategy to increase uptake of PCMHI when delivered on-site at larger VA clinics, it is hypothesized that this strategy may also be effective with regard to ensuring adequate uptake of the tele-PCMHI model at rural VA clinics. Methods This study is a hybrid type 2 pragmatic effectiveness-implementation trial of tele-PCMHI in six sites over 24 months. Tele-PCMHI, which will be delivered by clinical staff available in routine care settings, will be compared to usual care. Fidelity to the care model will be monitored but not controlled. We will use the Reach Effectiveness Adoption Implementation Maintenance (RE-AIM) framework to evaluate the patient-level clinical effectiveness of tele-PCMHI in rural VA clinics and also to evaluate the fidelity to and outcomes of the implementation strategy, implementation facilitation. The proposed study will employ a stepped-wedge design in which study sites sequentially begin implementation in three steps at 6-month intervals. Each step will include (1) a 6-month period of implementation planning, followed by (2) a 6-month period of active implementation, and (3) a final period of stepped-down implementation facilitation. Discussion This study will evaluate the effectiveness of PCMHI in a novel setting and via a novel method (clinical video telehealth). We will test the feasibility of using implementation facilitation as an implementation strategy to deploy tele-PCMHI in rural VA clinics. Trial registration ClinicalTrials.gov registration number NCT02713217. Registered on 18 March 2016 Electronic supplementary material The online version of this article (10.1186/s13012-019-0875-5) contains supplementary material, which is available to authorized users.