Several studies that aim to enhance the understanding of malaria transmission and persistence in urban settings failed to address its underlining complexity. We aim at doing that by applying a qualitative and participatory-based system analysis and mapping to elicit the system’s emergent properties. In two experts’ workshops, we sketched and refined the system, which was represented through a causal loop diagram, where the identification of leverage points was done using network analysis. We found 45 determinants interplaying through 56 linkages, and identified three subsystems: urbanization-related transmission, infection-prone behavior and healthcare efficiency, and Plasmodium resistance. Apart from the number of breeding sites and malaria positive cases, other determinants such as drug prescription and the awareness of householders were identified by the network analysis as leverage points and emergent properties of the system of transmission and persistence of malaria. Based on our findings, we suggest that ongoing efforts to control malaria, such as the use of insecticide-treated bed nets and larvicide applications should continue, and include new ones focusing on the public awareness and malaria literacy of city dwellers. We found that our participatory approach strengthened the legitimacy of the recommendations and the co-learning of participants.