Oxygen deficient zones (ODZs) in the tropical ocean exert a profound influence on global biogeochemical cycles, but the factors that regulate their long‐term structure and sensitivity to oceanic change remain poorly understood. We analyzed hydrographic observations and a high‐resolution physical/biogeochemical model to diagnose the primary pathways that ventilate the tropical Pacific ODZs. Historical and recent autonomous observations reveal pronounced and widespread O2 peaks, termed secondary oxygen maxima (SOMs), within the depths of the broader O2 minimum layer, especially at the equatorward edge of both northern and southern ODZs. In the northern ODZ, Lagrangian particle tracking in an eddy‐permitting numerical model simulation attributes these features to intrusions of the Northern Subsurface Countercurrent along the equatorial edge of the ODZ. Zonal subsurface jets also ventilate the poleward edge of the northern ODZ but induce a smaller O2 flux and do not yield detectable SOMs. Along the ODZ's eastern boundary, oxygenation is achieved by the seasonal cycle of upwelling of low‐O2 water onto the continental shelf, followed by downwelling of O2‐replenished near‐surface waters back into the ODZ. Waters entering the northern Pacific ODZ originate from the extratropics in both hemispheres, but two thirds are from the Southern Hemisphere and arrive later and with a wider range of transit times. These results suggest that predicting future changes in the large Pacific ODZs will require a better understanding of the climate sensitivity of the narrow zonal jets and seasonal dynamics of coastal upwelling that supply their O2.