As extreme climate events are predicted to become more frequent due to global climate change, understanding their impacts on natural systems is crucial. Tropical forests are vulnerable to droughts associated with extreme El Niño events. However, little is known about how tropical seedling communities respond to El Niño-related droughts, even though patterns of seedling survival shape future forest structure and diversity. Using long-term data from eight tropical moist forests spanning a rainfall gradient in central Panama, we show that community-wide seedling mortality increased by 11% during the extreme 2015-16 El Niño, with mortality increasing most in drought sensitive species and in wetter forests. These results indicate that severe El Niño-related droughts influence understory dynamics in tropical forests, with effects varying both within and across sites. Our findings suggest that predicted increases in the frequency of extreme El Niño events will alter tropical plant communities through their effects on early life stages.