BACKGROUND: By expanding primary health care services, Ethiopia has reduced under-five mor4tality. Utilisation of these services is still low, and concerted efforts are needed for continued improvements in newborn and child survival. "Optimizing the Health Extension Program" is a complex intervention based on a logic framework developed from an analysis of barriers to the utilisation of primary child health services. This intervention includes innovative components to engage the community, strengthen the capacity of primary health care workers, and reinforce the local ownership and accountability of the primary child health services. This paper presents a protocol for the process and outcome evaluation, using a pragmatic trial design including before-and-after assessments in both intervention and comparison areas across four Ethiopian regions. The study has an integrated research capacity building initiative, including ten Ph.D. students recruited from Ethiopian Regional Health Bureaus and universities. METHODS: Baseline and endline surveys 2 years apart include household, facility, health worker, and district health office modules in intervention and comparison areas across Amhara, Southern Nations Nationalities and Peoples, Oromia, and Tigray regions. The effectiveness of the intervention on the seeking and receiving of appropriate care will be estimated by difference-in-differences analysis, adjusting for clustering and for relevant confounders. The process evaluation follows the guidelines of the UK Medical Research Council. The implementation is monitored using data that we anticipate will be used to describe the fidelity, reach, dose, contextual factors and cost. The participating Ph.D. students plan to perform in-depth analyses on different topics including equity, referral, newborn care practices, quality-of-care, geographic differences, and other process evaluation components. DISCUSSION: This protocol describes an evaluation of a complex intervention that aims at increased utilisation of primary and child health services. This unique collaborative effort includes key stakeholders from the Ethiopian health system, the implementing non-governmental organisations and universities, and combines state-of-the art effectiveness estimates and process evaluation with capacity building. The lessons learned from the project will inform efforts to engage communities and increase utilisation of care for children in other parts of Ethiopia and beyond. TRIAL REGISTRATION: Current Controlled Trials ISRCTN12040912, retrospectively registered on 19 December, 2017.