The tectono‐sedimentary evolution of asymmetric extensional systems driven by the activity of major normal faults or detachments associated with footwall exhumation is often characterized by a sequence of slower, faster, and ultimately again slower subsidence rates in the center of hanging wall half‐grabens during their synkinematic and postkinematic evolution. We have studied this specific evolution by the means of 3‐D stratigraphic numerical modeling that accounts for the variability of the sediment and water flux combined with climatic and sea level variations, and sediment compaction. The model setup is constrained by observations from the Pannonian back‐arc basin of central Europe. Our modeling predicts the formation of low‐order tectonic and higher‐order sea level and climate‐driven transgressive‐regressive sedimentary cycles. Furthermore, we model and analyze the autocyclic nature of the depositional systems. Retrograding‐prograding cycles are visible on the proximal flank of the half‐grabens by their different spatial and temporal expressions, while depocenters record large water depth variations linked to the specific and episodic activity of normal faults and their migration with time. The application to a system of multiple half‐grabens in the Pannonian Basin, which are activated in different locations, at different times and with different kinematics, demonstrates a complex interplay between direct sediment sourcing and the sediments' ability to bypass trapping subbasins and paleo‐reliefs created by eroded footwalls. Plain Language Summary The formation and evolution of sedimentary basins is of prime interest as they record different Earth processes. The understanding of rifting mechanics and associated evolution of extensional sedimentary basins is also important for the assessment of their potential for georesources including freshwater. The spatial and temporal variabilities of vertical movements in asymmetric extensional systems control landscape evolution coupled to sedimentary and climatic processes. This paper aims to quantify the effect of tectonics and climatic variations on the overall architecture of such basins. Our numerical modeling demonstrates the low‐order tectonic and higher‐order sea level and climate‐driven influence on the sedimentary transport routes and overall architecture. The application of our model in the Pannonian Basin of central Europe shows how tectonic inheritance control sedimentary transport routes. Key Points Quantification of tectonic and climatic controls on sedimentation in asymmetric extensional basins New insights into distribution of lithologies, sedimentary facies, and unconformities in half‐grabens Verifying the new insights in the Pannonian Basin tectono‐sedimentary evolution