Background World-wide, health service providers are moving towards innovative models of clinical home-based care services as a key strategy to improve equity of access and quality of care. To optimise existing and new clinical home-based care programs, evidence informed approaches are needed that consider the complexity of the health care system across different contexts. Methods We present a protocol for working with health services and their partners to perform rapid identification, prioritisation, and co-design of content-appropriate strategies to optimise the delivery of healthcare at home for older people in rural and regional areas. The protocol combines Systems Thinking and Implementation Science using a Consensus Mapping and Co-design (CMC) process delivered over five workshops. Discussion The protocol will be implemented with rural and regional healthcare providers to identify digital and non-digital solutions that have the potential to inform models of service delivery, improve patient experience, and optimise health outcomes. The combination of system and implementation science is a unique approach for optimising healthcare at home for older populations, especially in the rural context where need is high. This is the first protocol to integrate the use of systems and implementation science into one process and articulating these methods will help with replicating this in future practice. Results of the design phase will translate into practice through standard health service planning methods to enhance implementation and sustainability. The delivery of the protocol will include building capacity of health service workers to embed the design, implementation, and evaluation approach into normal practice. This protocol forms part of the DELIVER (Delivering Enhanced heaLthcare at home through optImising Virtual tools for oldEr people in Rural and regional Australia) Project. Funded by Australia’s Medical Research Future Fund, DELIVER involves a collaboration with public health services of Western Victoria, Australia.