This paper aimed at improving the lack of GIS information use and compatibility of multiplatform which represented limits that existing malaria risk analysis tools had. For this, the author developed mobile web-based malaria vulnerability map system using GIS information. This system consists of system database construction, malaria risk calculation function, visual expression function, and website and mobile application. This system was developed based on Incheon region only. Database includes information on air temperature and amount of precipitation as well. With regard to malaria risk calculation, guideline provided by Korea Centers for Disease Control and Prevention was followed first and then decision-making technique was used. Calculating criteria value for risk index made it possible to estimate more precise risk. With regard to visual expression function, database constructed earlier and risk information were linked to print out graphic map and graphs so that more intuitive and visible expression can be provided based on animation technique. This system allows a user to check information in real time and can be used anywhere anyplace. Mobile push function is to enhance user’s convenience. Such web map is useful to general users as well as experts.