Schistosomiasis is recognised as a major public health problem in Rwanda. We aimed to identify the spatio-temporal dynamics of its distribution at a fine-scale spatial resolution and to explore the impact of control programme interventions. Incidence data of Schistosoma mansoni infection at 367 health facilities were obtained for the period 2001-2012. Disease cluster analyses were conducted using spatial scan statistics and geographic information systems. The impact of control interventions was assessed for three distinct sub-periods. Findings demonstrated persisting, emerging and re-emerging clusters of schistosomiasis infection across space and time. The control programme initially caused an abrupt increase in incidence rates during its implementation phase. However, this was followed by declining and disappearing clusters when the programme was fully in place. The findings presented should contribute to a better understanding of the dynamics of schistosomiasis distribution to be used when implementing future control activities, including prevention and elimination efforts.