Simple Summary Kenya has experienced an increased disease burden due to cholera outbreaks characterized by continuous transmission in the refugee camp settings of Garissa and Turkana, and sporadic transmission in cities such as Nairobi and Mombasa. However, while inquiry has been made regarding how the health sector has responded to and how populations have been impacted by epidemics such as cholera, not enough attention has been paid to causal relationships between the unique components of the health systems leading to an inadequate understanding of how the building blocks of the health systems interact in disease surveillance and epidemic response. Consequently, this research effort focuses on examining the health sector responses to these epidemics, developing a systems-theory-based description of the said responses, and based on the results, provide recommendations that may help break the epidemic's continuous and cyclical nature. The study will be conducted in Turkana and Garissa in Kenya, as well as in Nairobi. These are counties that have diverse levels of health system sophistication and recent experiences of cholera epidemics. Moreover, the study draws on several systems analytic frameworks to determine the actors and their decisions, as well as their inter-relationships, linkages and dependencies. Thus, the study appropriates systems-oriented research techniques and applies them in a novel fashion to the assessment of health service delivery. The findings of this study are expected to guide interventions aimed at improving disease surveillance and epidemic response. The study will also act as a primer for the research community by assessing the utility of systems-thinking approaches in such settings, and subsequently opening a related research agenda.