The results of petroleum system models (PSM) critically depend on the computed evolution of the temperature field. Because PSM typically only resolve the sedimentary basin and not the entire lithosphere, it is necessary to apply a basement–heat-flow boundary condition inferred from well data, surface–heat-flow measurements, and an assumed tectonic scenario. The purpose of this paper is to assess the use of surface–heat-flow measurements to calibrate basin models. We show that a simple relationship between surface and basement heat flow only exists in thermal steady state and that transient processes such as rifting and sediment deposition will lead to a decoupling. We study this relationship in extensional sedimentary basins with a one-dimensional, lithosphere-scale finite element model. The numerical model was built to capture the large-scale dynamic evolution of the lithosphere and simultaneously solve for transient thermal processes in basin evolution, such as sedimentation, compaction-driven fluid flow, and seafloor temperature variations. Our analysis shows that several corrections need to be applied when using surface–heat-flow information for the calibration of basement heat flow in PSM. Not doing so can lead to significant errors of up to 30°C–50°C (86°F–122°F) at typical petroleum-reservoir and source-rock depths. We further show that resolving sediment-blanketing effects in basin modeling is crucial, with the thermal impact of sediment deposition being at least as important as rifting-induced basement–heat-flow variations.