Magnetic surveys at tectonic windows that expose magnetic polarity boundaries provide the unique opportunity to explore the pattern of magnetization variations within the oceanic crust and determine the spatially averaged magnetizations of source layers that contribute to marine magnetic anomalies. Here we investigate the C2An.2n/C2An.2r polarity boundary in the tectonic window of Pito Deep, which has exposed a cross‐section through lavas, dikes, and the uppermost kilometer of gabbros at fast‐spread ocean crust. Near‐bottom magnetic anomaly surveys from two expeditions have been incorporated into a penalized least squares inversion method. The application of this method to magnetic data allows us to account for complex bathymetry and differing observation altitudes. When correlated with rock type, the magnetization solution shows median values of 4.4 ± 2.7 A/m for lavas, 2.0 ± 1.9 A/m for dikes, and 1.9 ± 1.9 A/m for gabbros. On a regional scale, lavas and dikes have a different polarity of magnetization than the underlying gabbros. The geometry of the polarity boundary is compatible with a large (~6 km) horizontal offset or very shallow dip of isotherms at the dike/gabbro boundary, and indicates that the zone of melt is significantly wider across axis than predicted from seismic tomography models that suggest pervasive cooling throughout the lower crust within a few kilometers of the spreading center.