Following the decline of Japanese eel catches and the EU European eel trade ban, other regions, such as Southeast Asia, have become increasingly important sources of juvenile anguillid species for aquaculture. Although appropriate fishery management of tropical eel species is urgently required, data collection by the government or scientific authorities is extremely difficult, because tropical glass eel fisheries are small-scale fisheries conducted in the Global South, where expertise and resources are sometimes limited. To collect data on glass eel fisheries, participatory stock assessments were conducted in West Java, Indonesia, where a Fishery Improvement Project (FIP) and an Aquaculture Improvement Project (AIP) were launched in collaboration with industries, middlemen, fishermen, NGOs, national and local agencies, and scientists. This participatory study successfully collected data on more than 3000 daily fishing practices from approximately 400 fishermen in a single water system in 2019. Even though the assessment was not species-specific, the data collected allowed estimation of the natural mortality rate as being 0.011 day−1. The annual exploitation rate of the glass eel fisheries was estimated as 24.9%, based on a generalised depletion model developed for the data-limited situation where only fishery catch and effort data are available. The data collection scheme for glass eel fisheries was disseminated by local and national agencies to glass eel fishermen in Indonesia and contributed to developing the Eel Conservation National Action Plan.