Abstract Timing is a key data for understanding the origin of faulting. The Balcones fault system (BFS) extends ~600 km along the northern margin of the Gulf of Mexico oil basin and controls springs that supply the major cities in Texas, but its origin is unclear. We provide its first direct timing by applying U–Pb geochronology on seven calcite‐mineralized fault surfaces. We have found that this extensional fault system formed during the Palaeocene‐middle Eocene time (from 61.3 ± 2.7 to 45.4 ± 2.1 Ma), which is much earlier than previous estimates. We show that the formation of the BFS coincides with the largest clastic influx in the northern Gulf of Mexico basin that resulted from Laramide uplift and erosion. This timing and the location of the BFS along the Ouachita suture, support our interpretation of this fault system formed as the result of lithospheric flexure related to Paleogene sedimentary loading.