The Pea Ridge iron oxide-apatite (IOA) deposit is one of the major rhyolite-hosted magnetite deposits of the St. Francois Mountains terrane, which is located within the Mesoproterozoic (1.5–1.3 Ga) Granite-Rhyolite province in the U.S. Midcontinent. Precise and accurate determination of the timing and duration of oreforming processes in this deposit is crucial for understanding its origin and placing it within a deposit-scale and regional geologic context. Apatite and monazite, well-established U-Pb mineral geochronometers, are abundant in the Pea Ridge orebody. However, the potential presence of multiple generations of dateable minerals, processes of dissolution-reprecipitation, and occurrence of micrometer-sized intergrowths and inclusions complicate measurements and interpretations of the geochronological results. Here, we employ a combination of several techniques, including ID-TIMS and high spatial resolution geochronology of apatite and monazite using LA-SC-ICPMS and SHRIMP, and Pb isotope geochemistry of pyrite and magnetite to obtain the first direct age constraints on the formation and alteration history of the Pea Ridge IOA deposit. The oldest apatite TIMS 207Pb*/206Pb* dates are 1471 ± 1 and 1468 ± 1 Ma, slightly younger than (but within error of) the ~1474 to ~1473 Ma U-Pb zircon ages of the host rhyolites. Dating of apatite and monazite inclusions within apatite provides evidence for at least one younger metasomatic event at ~1.44 Ga, and possibly multiple superimposed metasomatic events between 1.47 and 1.44 Ga. Lead isotop analyses of pyrite show extremely radiogenic 206Pb/204Pb ratios up to ~80 unsupported by in situ U decay. This excess radiogenic Pb in pyrite may have been derived from the spatially associated apatite as apatite recrystallized several tens of million years after its formation. The low initial 206Pb/204Pb ratio of ~16.5 and 207Pb/204Pb ratio of ~15.4 for individual magnetite grains indicate closed U-Pb system behavior in this mineral and are consistent with derivation of the Pb from a mantle-like source.