Malaria is currently an endemic disease in Mexico. The country joined the WHO’s E-25 initiative for the elimination of Plasmodium vivax to achieve elimination and certification within the established period. Having a Web-based information system was, therefore, deemed necessary to assist in the detection, investigation, and elimination of transmission in the foci, as well as for the timely treatment of malaria-positive cases. The “Information System for the Elimination of Malaria in Mexico” was designed, developed, and implemented with a geographic vision, which includes a Web tool to georeference homes and aquatic systems, a dashboard and an indicator evaluation card for monitoring activities, notification of probable cases, and vector control among other indicators. The implementation of the system was gradual in the seven states that are currently in the malaria elimination phase; subsequently, the system was implemented in non-transmission states. In 2020, the system implementation stage began; first, the basic data of more than 96,000 homes throughout the country were georeferenced, and then the primary data capture tools of 17 formats, 32 reports, and 2 geographic viewers were enabled for information queries. A total of 56 active foci have been identified in 406 localities as well as 71 residual foci in 320 localities. Recently, the Foci Manager was developed, which is a specific tool for the study, evaluation, and monitoring of active foci through a GIS, a dashboard, and a systematized evaluation certificate. Georeferencing tools decreased the cost of spatial data collection.