In recent times, there has been an increasing drive to demonstrate value for money (VfM) for investments made in public health globally. However, there is paucity of information on practical insights and best practices that have helped implementing organisations to successfully embed VfM in practice for programming and evaluation. In this article, we discuss strengths and weaknesses of approaches that been used and insights on best practices to manage for, demonstrate, and compare VfM, using a health pooled fund programme implemented in conflict-affected South Sudan as case study supported by evidence reported in the literature while critiquing adequacy of the available approaches in this setting. An expanded and iterative process framework to guide VfM embedding for health programming and evaluation is then proposed. In doing so, this article provides a very relevant one-stop source for critical insight into how to embed VfM in practice. Uptake and scale-up of the proposed framework can be essential in improving VfM and aid effectiveness which will ultimately contribute to progress towards achieving the Sustainable Development Goals by 2030.