Two dimensional (2D) and (3D) seismic data integrated with outcrops and well logs are used to provide new insights on the structural geometry and tectonic evolution of the Gulf of Suez and the Egyptian Red Sea rift system. Surface analogues of Gebel El Zeit and Gebel Duwi along the western coast of the Gulf of Suez-Red Sea offer distinctive model for the syn- and pre-rift structural and stratigraphic patterns. Theses exposures have significant control on equivalent successions extending in the offshore. The syn-rift sedimentary successions attain an average thickness of ~ 4 km in offshore penetrations. The pre-rift successions were extensively drilled in the Gulf of Suez, and were encountered in the tunnels, mines and cores along Red Sea onshore area in Egypt’s Eastern Desert. These intervals are sporadically cropping out in the Gebel Duwi area. Integration of surface and subsurface geology provided coherent pattern of the fault complex and the comprehensive relations of fault linkage and transfer zones affecting the Precambrian basement rocks. Seismic sections and subsurface mapping of top basement and Miocene levels show large rotated fault blocks bounded by NW–SE oriented master faults (Clysmic trend) and dissected by NE-SW fault system parallel to Aqaba trend. The tectonic evolution of this rift system is mainly controlled by the rising of Afar plume and the rotation of Arabia to the NW direction in response to the separation from the African plate. The multiphase extensional history of the basins is indicated by seismic cross-section restoration and detailed subsurface mapping. The first stage of rifting in the Red Sea occurred during the early to early middle Miocene, from about Aquitanian to serravalian. During that time Red Sea and Gulf of Suez initiated as single narrow elongate basin. The deposition of the Lower Miocene Burdigalian Rudeis Formation experienced high rate of extension and subsidence. The mid-Clysmic unconformity, together with a younger Middle Miocene (Serravallian) post-Kareem unconformity resulted from the restriction of large extension to the Red Sea through the development of the Aqaba-Levant Strike-Slip Fault Zone. Then, the evolution of the Gulf of Suez was dominated by thermally driven subsidence with only limited extension. A phase of large-scale extension was continued in the southern Red Sea. Finally, during the termination of the basin tectonics in the Tertiary, the main structures were dominated by the NNW-SSE trend. The principal direction of extension during the opening of the rift was orthogonal to slightly oblique to this trend.