Background: The importance of civil society organisations in health care delivery systems cannot be under-rated in sub-Saharan Africa and other developing nations worldwide. Civil society organisations play a central role in service delivery and development of democracy. However, little is known about the roles and achievements of Civil Society Organisations (CSOs) in healthcare. The study aimed at exploring the role of civil society organisations in health care delivery system particularly in children immunization. Methods: A questionnaire survey involving 282 households was conducted. Data were analysed using descriptive statistics followed by multivariable logistic regression. Results: Ninety seven percent (97%) confirmed that CSOs/NGOs healthcare facilities played a major role in healthcare service delivery. 84% travelled long distances to access the healthcare services including child immunisation services. Travelling long distances (>2 km) to access for health care services including immunization compared to short distance (<1 km) (OR = 0.4, P = 0.0001), possessing a food stores (enguli) compared to not having a food store (enguli) (OR = 2.3, P = 0.002), having separate animal houses compared to not having livestock houses (OR = 0.09, P = 0.0001), and owning a bicycle compared to not having a bicycle (OR = 2.2, P = 0.005) are important determinants for the number of clients at CSO health centers. Further, possessing and using a cellphone compared to no cellphone (OR = 3.7, P = 0.001), Possessing and watching a television compared to not having a television (OR = 2.4, P = 0.002), educated compared to not acquiring any formal education (OR = 0.084, P = 0.0001), and female compared to male respondent (OR = 0.49, P = 0.0045) are other most important factors likely to determine the numbers of clients at the CSO healthcare. Conclusion: Geographies of CSO and community socioeconomics strongly determine the operations and the roles played by the CSO healthcare services in Uganda. Further studies to assess the role of CSO health service providers in other healthcare services need to be done.