Mountain Pass is the site of the most economically important rare earth element (REE) deposit in the United States. Mesoproterozoic alkaline intrusions are spatiotemporally associated with a composite carbonatite stock that hosts REE ore. Understanding the genesis of the alkaline and carbonatite magmas is an essential scientific goal for a society in which critical minerals are in high demand and will continue to be so for the foreseeable future. We present an ion microprobe study of zircon crystals in shonkinite and syenite intrusions to establish geochronological and geochemical constraints on the igneous underpinnings of the Mountain Pass REE deposit. Silicate whole-rock compositions occupy a broad spectrum (50–72 wt % SiO₂), are ultrapotassic (6–9 wt % K₂O; K₂O/Na₂O = 2–9), and have highly elevated concentrations of REEs (La 500–1,100× chondritic). Zircon concordia ²⁰⁶Pb/²³⁸U-²⁰⁷Pb/²³⁵U ages determined for shonkinite and syenite units are 1409 ± 8, 1409 ± 12, 1410 ± 8, and 1415 ± 6 Ma (2σ). Most shonkinite dikes are dominated by inherited Paleoproterozoic xenocrysts, but there are sparse primary zircons with ²⁰⁷Pb/²⁰⁶Pb ages of 1390–1380 ± 15 Ma for the youngest grains. Our new zircon U-Pb ages for shonkinite and syenite units overlap published monazite Th-Pb ages for the carbonatite orebody and a smaller carbonatite dike. Inherited zircons in shonkinite and syenite units are ubiquitous and have a multimodal distribution of ²⁰⁷Pb/²⁰⁶Pb ages that cluster in the range of 1785–1600 ± 10–30 Ma. Primary zircons have generally lower Hf (<11,000 ppm) and higher Eu/Eu* (>0.6), Th (>300 ppm), Th/U (>1), and Ti-in-zircon temperatures (>800°C) than inherited zircons. Oxygen isotope data reveals a large range in δ¹⁸O values for primary zircons, from mantle (5–5.5‰) to crustal and supracrustal (7–9‰). A couple of low-δ¹⁸O outliers (2‰) point to a component of shallow crust altered by meteoric water. The δ¹⁸O range of inherited zircons (5–10‰) overlaps that of the primary zircons. Our study supports a model in which alkaline and carbonatite magmatism occurred over tens of millions of years, repeatedly tapping a metasomatized mantle source, which endowed magmas with elevated REEs and other diagnostic components (e.g., F, Ba). Though this metasomatized mantle region existed for the duration of Mountain Pass magmatism, it probably did not predate magmatism by substantial geologic time (>100 m.y.), based on the similarity of 1500 Ma zircons with the dominantly 1800–1600 Ma inherited zircons, as opposed to the 1450–1350 Ma primary zircons. Mountain Pass magmas had diverse crustal inputs from assimilation of Paleoproterozoic and Mesoproterozoic igneous, metaigneous, and metasedimentary rocks. Crustal assimilation is only apparent from high spatial resolution zircon analyses and underscores the need for mineral-scale approaches in understanding the genesis of the Mountain Pass system.