Introduction: Delays in case-based surveillance are a significant obstacle to eliminating malaria. This study aims to optimise the current electronic malaria information system (eMIS), which uses an eMIS android-based mobile. Method: Qualitative research was conducted in the Lahat District, South Sumatra Province. We select informants directly involved in, or playing a role in, malaria control activities, such as program managers at community health centres (Puskemas) and health services. The system is built using the Framework for the Application of Systems Techniques (FAST), a structured method for analysing complex systems. It helps professionals break down problems, uncover hidden relationships, and make better decisions. FAST is widely used in engineering, project management, and business process optimisation to tackle complex challenges and improve problem-solving. Results: The paper revealed suggestions for designing and optimising the current eMIS. One recommended method for overcoming the obstacles is to optimise an eMIS Android-based mobile for malaria reporting. Eight key informants participated in the interviews. The main obstacles by key informants are the free time available for giving deep information and annoyance from outside during interviews due to their other activities. Hence, the researchers made appointments with informants and interviewed in a particular room, not the informant’s office. Conclusion: Our study demonstrates that eMIS android-based mobile is a better refinement of the current eMIS based on PC to support malaria surveillance for malaria elimination programs in an endemic area. Data entry with an eMIS android-based mobile is faster, more accurate, and allows real-time collaboration, outperforming sheet applications.