Simulation modeling is increasingly being used for strategy implementation, policy analysis and design in healthcare management. Preventable childhood diseases and premature deaths still occur particularly in the developing countries despite the various approaches that have been applied to understand immunisation coverage problems. While the immunisation system like other healthcare systems is complex, the System Dynamics modeling approach is applied and tested on the Ugandan healthcare system. Results of the study show that, the population, healthcare and vaccine management policies have overwhelming in?uence on immunisation coverage and form the foundations on which the success of immunisation policy is based. The developed models demonstrate the dynamics and test different policies thus making it useful for strategic planning and policy debate. Suggested intervention strategies that could provide substantial effect on immunisation coverage include: strengthening of the healthcare system, design of relevant health information systems, adoption of ICTs innovations to improve operational efficiency and improvement of the livelihood of the population.