The lack of knowledge about the enrichment mechanism of rare earth elements and yttrium (REY) in deep-sea sediments is impeding the development of theories and exploration strategies for pelagic REY-rich sediments. Ocean circulation variability seems to be crucial in enriching REY in pelagic sediments, which, however, has not been extensively studied. Here, we examined the Pb-Nd isotopic signals of bottom water recorded by the authigenic ferromanganese oxyhydroxide fractions, as well as the Mn/Al and Mn/Ti ratios of bulk samples from a well-dated sediment core in the northwestern Pacific Ocean. These proxies consistently indicate that enhanced deep-water circulation occurred in the study area at ∼11.5–9.5 Ma, which was most likely to be caused by changes in the flow path of bottom currents. The age of this distinct event consists with the forming age of highly REY-rich sediments. We propose that enhanced deep-water circulation in seamount areas could increase the flux of micronodules and fish debris into the pelagic sediments, facilitating the scavenging of REY from seawater. Our findings establish a connection between enhanced deep-water circulation and the enrichment of REY in pelagic sediments.