There is a growing recognition that the global health agenda needs to shift from an emphasis on disease-specific approaches to strengthening of health systems. Building leadership, management and governance capacities within the healthcare systems provides an opportunity to strengthen healthcare workforce, improve program performance, develop relationships with target populations and enhance the ability of the health system to respond quickly and effectively to change. The objective of this study was to investigate healthcare systems and institutional performance vulnerability and variance to leadership and governance interventions in IPPF Ghana and Kenya Chapters. In order to achieve this main objective, the following specific objectives were laid down; to identify health leadership and governance vulnerability and variance facing the IPPF Ghana and Kenya chapters, to describe the variations in the implementation process in IPPF Ghana and Kenya Chapters and to describe potential contributors to the disparity in performance between the Ghanaian and Kenyan chapters of IPPF.. The study used a survey research design (survey monkey) to target 90 participants, 57 senior management staff and 33 national governing board members in IPPF Ghana and Kenya Chapters. Data was collected from 67 respondents (74.5%) out of a total of 90 participants in both IPPF Ghana and Kenyan Chapters using the administration of a questionnaire which had closed and open ended questions. An analysis of the data was conducted using descriptive method and the coding was drawn from the USAID/MSH/IPPF methodology (Yes=2), (No=1) and (N/A=0). Particular attention focusing on strong management systems as highlighted in the USAID/MSH leading, managing and governing for results conceptual framework and further, an exploration on how these interactions contributed towards strong healthcare systems was brought to light.