Seismic rays traveling just below the Moho provide insights into the thermal and compositional properties of the upper mantle and can be detected as Pn phases from regional earthquakes. Such phases are routinely identified in the continents, but in the oceans, detection of Pn phases is limited by a lack of long‐term instrument deployments. We present estimates of upper‐mantle velocity in the equatorial Atlantic Ocean from Pn arrivals beneath, and flanking, the Mid‐Atlantic Ridge and across several transform faults. We analyzed waveforms from 50 earthquakes with magnitude , recorded over 12 months in 2012–2013 by five autonomous hydrophones and a broadband seismograph located on the St. Peter and St. Paul archipelago. The resulting catalog of 152 ray paths allows us to resolve spatial variations in upper‐mantle velocities, which are consistent with estimates from nearby wide‐angle seismic experiments. We find relatively high velocities near the St. Paul transform system (), compared with lower ridge‐parallel velocities (). Hence, this method is able to resolve ridge‐transform scale velocity variations. Ray paths in the lithosphere younger than 10 Ma have mean velocities of , which is slightly lower than those sampled in the lithosphere older than 20 Ma (). There is no apparent systematic relationship between velocity and ray azimuth, which could be due to a thickened lithosphere or complex mantle upwelling, although uncertainties in our velocity estimates may obscure such patterns. We also do not find any correlation between Pn velocity and shear‐wave speeds from the global SL2013sv model at depths . Our results demonstrate that data from long‐term deployments of autonomous hydrophones can be used to obtain rare and insightful estimates of uppermost mantle velocities over hundreds of kilometers in otherwise inaccessible parts of the deep oceans.