We present a generic algorithm for automating sedimentary basin reconstruction. Automation is achieved through the coupling of a two-dimensional thermotectonostratigraphic forward model to an inverse scheme that updates the model parameters until the input stratigraphy is fitted to a desired accuracy. The forward model solves for lithospheric thinning, flexural isostasy, sediment deposition, and transient heat flow. The inverse model updates the crustal- and mantle-thinning factors and paleowater depth. Both models combined allow for automated forward modeling of the structural and thermal evolution of extensional sedimentary basins. The potential and robustness of this method is demonstrated through a reconstruction case study of the northern Viking Graben in the North Sea. This reconstruction fits present stratigraphy, borehole temperatures, vitrinite reflectance data, and paleowater depth. The predictive power of the model is illustrated through the successful identification of possible targets along the transect, where the principal source rocks are in the oil and gas windows. These locations coincide well with known oil and gas occurrences. The key benefits of the presented algorithm are as follows: (2) crustal- and mantle- (1) only standard input data are required, thinning factors and paleowater depth are automatically computed, and (3) sedimentary basin reconstruction is greatly facilitated and can thus be more easily integrated into basin analysis and exploration risk assessment.