Introduction: Geographical information system (GIS) and spatial analysis have an emerging role in the understanding and management of health-related outcomes. However, there is a knowledge gap about the extent to which GIS has supported multiple Sclerosis (MS) research. Therefore, this review aimed to explore the types of GIS applications and the complexity of their visualisation in MS research. Methods: A systematic scoping review was conducted based on York's five-stage framework. PubMed, Scopus and Web of Science were searched for relevant studies published between 2000 and 2020 using a comprehensive search strategy based on the main concepts related to GIS and MS. Grounded, inductive analysis was conducted to organize studies into meaningful application areas. Further, we developed a tool to assess the visualisation complexity of the selected papers. Results: Of 3,723 identified unique citations, 42 papers met our inclusion criteria for the final review. One or more of the following types of GIS applications were reported by these studies: (a) thematic mapping (37 papers); (b) spatial cluster detection (16 papers); (c) risk factors detection (16 papers); and (d) health access and planning (two papers). In the majority of studies (88%), the score of visualisation complexity was relatively low: three or less from the range of zero to six. Conclusions: Although the number of studies using GIS techniques has dramatically increased in the last decade, the use of GIS in the areas of MS access and planning is still under-researched. Additionally, the capacity of GIS in visualising complex nature of MS care system is not yet fully investigated.