The value of engaging stakeholders for locally relevant responses and sustainable gains in disease control programs has been increasingly acknowledged. As opposed to a traditional top-down implementation of malaria intervention strategies, community bottom up initiatives require that all stakeholders be identified and strategies of engagement are designed at an early stage of program planning, implementation, and evaluation, to promote optimal intervention impact and program ownership and sustainability. A stakeholder analysis was conducted as part of a formative analysis in multiple community based studies under the malaria elimination program (MEPR) in Eastern Province of Rwanda. Starting with an initial list of stakeholders a snowball sampling technique was employed to identify other potential stakeholders from national and local public/private institutions and community/faith-based organizations. Individual interviews with nineteen stakeholders and eight focus group discussions with a total of 69 stakeholders were conducted. Stakeholders were classified into primary (lay community), secondary (local administrative and health institutions) and key stakeholders (policy makers and funders). Most of the stakeholders consulted were further classified depending on their type and degree of involvement unto information, consultation/collaboration, co-decision and empowerment categories. The MEPR team independently assigned participatory communication techniques to stakeholders for further engagement. In addition to awareness about MEPR activities, stakeholders’ reported willingness to contribute to the promotion of malaria preventive measures, participation in supportive hands-on trainings and in the MEPR planning (pre-engagement meetings and trainings), implementation (formative research and project interventions) and knowledge translation activities, such as the development of project materials as well as participation in lay and scientific workshops where research findings dissemination and interpretation were discussed. Overall, the analysis enabled the MEPR to know who to engage for a particular project activity and the appropriate time to do so. Stakeholders appreciated the early consultation by the MEPR and solicited continuous updates on malaria activities and key findings. Subsequently, stakeholder identification has been updated to evolve with shifting stakeholder interests over time.