The southern coast of Central Java Province is one of Indonesia’s largest eels (Anguilla spp.) fishing grounds. The annual eel catches in this region showed an increasing trend in 2011–2014 but then plummeted in 2019–2021. However, studies on stock status are lacking to provide an effective management plan to prevent the collapse of eel fisheries. Therefore, this study assessed the state of freshwater eels in Southern Central Java using a data-limited method, catch-based maximum sustainable yield (CMSY). The analysis revealed a swift stock depletion, shifting from a healthy state in 2011 to a concerning red zone in 2015–2018. Subsequently, the stock began a recovery phase in 2019, but the recent trajectory raised concerns as it approached the red zone again, signaling the urgency of implementing a rebuilding plan. The simulation of several rebuilding scenarios suggests that reducing fishing mortality to 80% of the FMSY (maximum sustainable fishing mortality) can balance production and conservation objectives, achieving the quickest stock rebuilding with minimal catch loss. This study showed that eel stock could be rebuilt by reducing fishing pressure to preserve a surplus of individuals who can complete their migration and spawning cycles.