The Pamplona Fault in the Pyrenees is a major transverse structure that has been classically interpreted as a strike-slip fault. However, lack of consensus concerning the sense of movement casts doubt on its actual kinematics and, as a consequence, its role in the Cenozoic evolution of the Pyrenees remains controversial. In order to assess its kinematics, we have conducted a paleomagnetic, structural, and stratigraphic study focused on the Mesozoic and Tertiary sedimentary rocks that outcrop around the southern segment of the fault. Restoration of balanced cross sections allows us to examine the present-day spatial relationship of the sedimentary sequences on both sides of the fault and to reconstruct the geometry of the extensional basins formed during Mesozoic rifting episodes in the Bay of Biscay and Pyrenean domains. Paleomagnetic results indicate that no significant tectonic rotations occurred around the fault during Tertiary inversion of the Pyrenees. The lack of tectonic rotations and revaluation of previous hypotheses argues against a strike-slip movement of the fault. We propose a new model in which the Pamplona Fault is treated as a large-scale hanging wall drop fault whose kinematics was determined by variations in the geometry and thickness of Mesozoic sequences on both sides of the fault. These variations influenced the geometry of the thrust sheet developed during Tertiary compression. We are unaware of any other transverse fault that has been interpreted in this fashion; thus the Pamplona Fault serves as a case study for the evolution of transverse faults involved in basin inversion processes.