Deep-sea mud enriched in rare-earth elements (REEs), termed REE-rich mud, is a promising seafloor mineral resource. A decade of surveys has revealed that the mud with the highest REE concentration occurs in the pelagic realm of the western North Pacific Ocean, with two layers of elevated REE concentration. Previous analyses of sediments have revealed multiple periods of significant REE enrichment, with the first (youngest) REE enrichment triggered by global cooling during the Eocene–Oligocene climate transition. However, the depositional mechanism of older REE peaks remains unclear. Fish debris is the major host of REE in deep-sea sediments. In this study, the microfossils of fish teeth and denticles, called ichthyoliths, were observed to constrain the depositional ages of REE-enriched layers with unknown genesis. Empowered by deep learning, more than 40,000 ichthyoliths were observed, and the second (older) REE enrichment was revealed to have occurred in the early Eocene, when the Earth’s climate was exceedingly warm. The warm ocean may have enhanced the efficiency of trophic transfer, leading to an increased supply of fish debris and thus REE, to the seafloor. Therefore, the Paleogene Hothouse might have been advantageous for producing valuable seafloor mineral resources.