BackgroundMalaria remains a significant public health issue in Indonesia. Most of the endemic areas are in the eastern parts of Indonesia, but there are a few remaining foci of persistent endemic malaria in Java, particularly in Menoreh Hills, a region bordering three districts of two provinces on this island. Despite a commitment to build a partnership to eliminate cross-border malaria, there is a lack of understanding of how this partnership might be translated into an implementable strategic plan. The study aims to provide evidence of how a participatory approach was used to strengthen the cross-border collaboration and stakeholders’ capacity to develop a joint strategic, operational, and costing plan for cross-border malaria elimination.MethodsA participatory action research was conducted from January to August 2017, involving participants from the village, district, provincial, and national levels. This study was conducted in seven phases, including document review, focus group discussions (FGDs), planning and costing workshops, and a dissemination meeting. A total of 44 participants from primary health centres (PHC) and 27 representatives of affected villages in three districts, 16 participants from the district and provincial malaria programmes and planning bureaus, and 11 participants from the national level were involved in the processes. Data on priority issues, costing, programme coverage, and administration were collected. Thematic coding and feedback were used for analysis.ResultsProblems identified by stakeholders included low community awareness and participation in malaria prevention, high mobility across three districts, lack of financial and human resources, lack of inter-district coordination, and poor implementation of migration surveillance. Cross-border strategies identified to address malaria were improving cross-border migration surveillance, strengthening the network, governance, and advocacy of malaria control implementation across borders, and developing the malaria information system. A working group composed of the three districts’ representatives authorized to decide on cross-border issues will be created.ConclusionsThe participatory approach was applicable in cross-border malaria planning for within-country settings and useful in enhancing stakeholders’ capacities as implementers. While done in a participatory way, the joint plan crafted was a non-binding agreement; stakeholders should advocate to ensure adequate funds are poured into mobilizing the programme.