The San Juan Basin located on the southeastern margin of the Colorado Plateau in northwestern New Mexico started to form during Laramide compression at 75 Ma and was episodically filled with sediments until late Eocene to Oligocene time. The basin lies in a unique geographic position. The middle Cenozoic San Juan volcanic field lies to the north, the Rio Grande rift is to the east, the Laramide Zuni uplift forms the southern margin, and the continental divide, which separates drainages that flow to the Colorado River from those that flow to the Rio Grande, crosses the basin. Furthermore, the basin is an important oil-producing province with abundant core and related geologic information. In this investigation, apatite fission-track (AFT) data from cores from thirteen wells from across the basin are used to evaluate the relative importance of tectonic and erosional exhumation in shaping the Laramide and post-Oligocene landscape of this region. The current thermal state of the San Juan Basin is evaluated using published equilibrium logs, industry wireline temperature logs, bottom-hole temperatures (BHT), and drill-stem test temperatures. The sedimentary architecture of the basin controls the thermal structure, and thus the inferred exhumation history of the basin. For example, the overall present-day geothermal gradient in the San Juan Basin is low (20–25°C/km), but locally the geothermal gradient is elevated in coal-bearing and in thick shale intervals, which have low thermal conductivity. AFT samples from wells that intersect the coal-bearing Late Cretaceous Fruitland Formation in the northern and central parts of the basin have unusually high modern temperatures and younger AFT ages in the older part of the section compared to areas to the south on the Chaco Slope, where the Fruitland was stripped by erosion related to the Laramide exhumation in the Zuni Mountains; the AFT ages from wells on the Chaco Slope record Laramide exhumation. Both published heat flow data and the industry temperature logs and BHT data analyzed during this study document elevated modern subsurface temperatures in the northern part of the basin, consistent with the elevated observed heat flow and the high modern elevation of the San Juan Mountains. Post-Oligocene exhumation ranges from ~500–1500 m and is highest in the San Juan River valley.