The location of the India-Arabia plate boundary prior to the formation of the Sheba ridge in the Gulf of Aden is a matter of debate. A seismic dataset crossing the Owen Fracture Zone, the Owen Basin, and the Oman Margin was acquired to track the past locations of the India-Arabia plate boundary. We highlight the composite age of the Owen Basin basement, made of Paleocene oceanic crust drilled on its eastern part, and composed of pre-Maastrichtian continental and oceanic crust overlaid by ophiolites emplaced in Early Paleocene on its western side. A major fossil transform fault system crossing the Owen Basin juxtaposed these two slivers of lithosphere of different ages, and controlled the uplift of marginal ridges along the Oman Margin. This transform system deactivated ∼40 Myrs ago, coeval with the onset of ultra-slow spreading at the Carlsberg Ridge. The transform boundary then jumped to the edge of the present-day Owen Ridge during the Late Eocene-Oligocene period, before seafloor spreading began at the Sheba Ridge. This migration of the plate boundary involved the transfer of a part of the Indian oceanic lithosphere formed at the Carlsberg Ridge to Arabia. This Late Eocene-Oligocene tectonic episode at the India-Arabia plate boundary is synchronous with a global plate reorganization event corresponding to geological events at the Zagros and Himalaya belts. The Owen Ridge uplifted later, in Late Miocene times, and is unrelated to any major migration of the India-Arabia boundary.