Mobile applications are promising tools for strengthening service quality and have been an area of considerable mHealth innovation. Despite growing demand for data to guide policymakers, donors, and program managers in making sound investments, there is a paucity of evidence on the cost-effectiveness of mHealth technologies. To address this gap, the HFG Project analyzed a mobile decision support tool with the following objectives: First, it aimed to provide a transparent and detailed methodology for categorizing the costs of building, deploying, and scaling-up mobile decision support tools in Malawi. Second, it evaluated the incremental cost-effectiveness of a mobile tool’s use in improving clinical care. Finally, the evaluation addressed challenges faced in conducting cost-effectiveness analyses of mHealth interventions when they are scaled up and become multifunctional.