Deep-sea sediments enriched in rare earth elements and yttrium (REY) are promising mineral resources and are extensively developed in the Pacific Ocean. However, REY enrichment mechanisms of deep-sea sediments remain poorly constrained due to a lack of chronological constraints on associated geological events. We integrated bioapatite U-Pb geochronometry with geochemical data to elucidate the temporal evolution and genetic processes of REY-rich sediments located in the Clarion-Clipperton Fracture Zone (CCFZ) in the central North Pacific Ocean. Fish tooth specimens, separated from deep-sea sediments collected from core MG026, were subjected to in situ trace-element analysis and U-Pb dating on their enamel-protected dentin layers using laser ablation−inductively coupled plasma−mass spectrometry. The bioapatite samples exhibited higher enrichments in total REY (ΣREY) and uranium than bulk sediments, and a moderate positive correlation between ΣREY and uranium concentrations. These bioapatite samples yielded Tera-Wasserburg lower intercept ages ranging from 15.8 ± 1.2 Ma to 9.5 ± 1.4 Ma, robustly constraining the depositional age of the host sediments and revealing a pronounced REY enrichment episode from 12.0 Ma to 9.0 Ma. Our results demonstrate a mean sedimentation rate of ∼0.48 m/m.y. for the REY-rich sediments in the CCFZ. Multivariate analysis of bulk geochemical data indicates that REY-enrichment in CCFZ sediments is controlled not only by slow deposition rate but also by REY-bearing mineral phases and depositional environment conditions (including redox conditions and biological productivity). The REY enrichment event (ca. 12.0−9.0 Ma) is characterized by a significant transition toward more oxygenated and higher productivity conditions, as documented by trace metal enrichment factors (EF) of Mo_EF, U_EF, Cu_EF, and Ni_EF. This event coincided with the progressive closure of the Central American Seaway, which enhanced the advection of oxygen-enriched, nutrient-bearing bottom waters into the CCFZ, promoting extensive formation of Fe-Mn (oxyhydr)oxides and facilitating REY enrichment. Our study establishes a reliable geochronological framework for late Miocene REY enrichment and provides exploration strategies linking tectonic events to deep-sea REY mineralization in the CCFZ.