BACKGROUND: Responsibility for planning and delivery of health services in the Philippines is devolved to the local government level. Given the recognised need to strengthen capacity for local planning and budgeting, we implemented Investment Cases (IC) for Maternal, Neonatal and Child Health (MNCH) in three selected sub-national units: two poor, rural provinces and one highly-urbanised city. The IC combines structured problem-solving by local policymakers and planners to identify key health system constraints and strategies to scale-up critical MNCH interventions with a decision-support model to estimate the cost and impact of different scaling-up scenarios. METHODS: We outline how the initiative was implemented, the aspects that worked well, and the key limitations identified in the sub-national application of this approach. RESULTS: Local officials found the structured analysis of health system constraints helpful to identify problems and select locally appropriate strategies. In particular the process was an improvement on standard approaches that focused only on supply-side issues. However, the lack of data available at the local level is a major impediment to planning. While the majority of the strategies recommended by the IC were incorporated into the 2011 plans and budgets in the three study sites, one key strategy in the participating city was subsequently reversed in 2012. Higher level systemic issues are likely to have influenced use of evidence in plans and budgets and implementation of strategies. CONCLUSIONS: Efforts should be made to improve locally-representative data through routine information systems for planning and monitoring purposes. Even with sound plans and budgets, evidence is only one factor influencing investments in health. Political considerations at a local level and issues related to decentralisation, influence prioritisation and implementation of plans. In addition to the strengthening of capacity at local level, a parallel process at a higher level of government to relieve fund channelling and coordination issues is critical for any evidence-based planning approach to have a significant impact on health service delivery.