West Africa's extensive migratory activities and unregulated cross-border community interactions pose public health challenges. Understanding cross-border community relations and interactions helps in emergency preparedness planning and response. We designed cross-sectional qualitative study, interviewing focus groups and key informants in contiguous border communities in Ghana and Burkina Faso. We assess if and how cross border interactions compromise or facilitate management of public health emergencies. And found that understanding and managing frontier community interactions, interrelationships and respectful dialogue among stakeholders within and between border communities is sine qua non for constructing a robust and responsive architecture for effective epidemic preparedness and control.