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Introduction The emergency medical disease burden in low-income countries such as Ethiopia is four times that of high-income countries. It is estimated that more than half of all deaths occurring in low-and-middle-income countries each year could be prevented by organised Emergency Care System but the emergency care in these countries is fragmented and unstructured. The WHO’s Emergency Care Systems (WHO-ECS) toolkit aims to systematise and structure emergency care in such countries. Objectives To identify and analyse key facilitators and barriers encountered during the implementation of the (WHO-ECS) toolkit in primary hospitals in Ethiopia, within the context of a national emergency care strengthening initiative.Methods This was a qualitative research arm of a larger implementation study conducted within 10 primary hospitals in the Oromia region, Ethiopia for 14 months. Qualitative data were collected using focus group discussions with healthcare workers in target hospitals (Amaya, Arsi Kersa, Tulu Bolo and Robe Dida Hospitals) selected via lottery method and key-informant questionnaires among project coordinators from May 2021 to February 2022. Facilitators and barriers to the implementation process were identified using thematic data analysis.Results There were 40 participants in four focus group discussions and four respondents to the key informant questionnaires. Facilitators of the toolkit included a supportive model of implementation, enthusiastic staff and the toolkit itself. Lack of medications and equipment, some components in the toolkit itself and lack of permanent staff in emergency departments were found to be barriers. Support from hospital administrators was a facilitator while lack thereof was a hurdle.Conclusion This study has outlined the significant factors related to implementing the WHO-ECS toolkit in a low-income setting. Support from project implementers and hospital administrators as well as key stakeholder involvement facilitates success. Conversely, lack of support and resources as well as toolkits misaligned with context can hamper it. Comparable healthcare setups can use these lessons before and during implementation.