Transforming the provision of healthcare involves collaboration and change on many levels. Too often healthcare delivery decisions are made without considering the complex and dynamic nature of the health system. Approaching these problems from a systems thinking perspective integrates these traits and encourages long term thinking about solutions. Despite being widely used in other disciplines, only recently has systems analysis started to play a larger role in transforming healthcare provision. The purpose of this work is to outline how systems analysis tools can bridge multiple levels of healthcare to make more informed decisions. The aforementioned will be illustrated using a Canadian case study. Currently, a provincial strategy to diagnose and treat epilepsy in adults and children in Ontario is being examined. The organization of epilepsy specific care centres (ESCC) into district and regional services is being recommended which will modify current practice patterns and access to care. Subsequently, any changes in delivery will have an impact on referral rates and patterns as well as resource utilization (i.e. beds, staff, and diagnostic tests). The use of systems analysis tools can bring insight into how the inter-relationship between ESCCs can be modeled and how access to care will be affected and aid in capacity planning (i.e. resources and costs).System changes can be graphically illustrated and quantified using the systems analysis tool discrete event simulation. Mapping the clinical pathways and patient flow of epileptic patients through the current system, a simulation model was developed to help inform the planning process. This was useful in understanding how the system might respond and in identifying potential bottlenecks or where resources may be limited. Using discrete event simulation facilitated the ability to take on multiple perspectives by conducting analyses at multiple institutional levels (i.e. government, hospital and health care practitioner).