The incision of kilometer-scale canyons into high-standing topography is often used to constrain the surface uplift history of mountain ranges, controlled by tectonic and geodynamic processes. However, changes in climate may also be responsible for canyon incision. This study deciphers the timing of incision of the ~2.5-km-deep Cauca River Canyon in the Central Cordillera of the Northern Andes using the cooling (exhumation) history of rocks from the canyon walls and a regional analysis of channel steepness in rivers. Ten bedrock samples and one detrital sample were collected on the eastern border of the canyon between 300 m and 2300 m of elevation. Bedrock and detrital AFT data yield ages from 50 to 38 Ma, while two bed-rock AHe ages from the valley bottom yield ages of 7–6 Ma. The AHe ages and inverse thermal history models reveal a previously unidentified late Miocene (ca. 7–6 Ma) pulse of exhumation that we interpret as the age of a single incision event that formed the Cauca River Canyon. We conclude that the Cauca River Canyon was carved as a response to rock uplift in the northern Central Cordillera and propagation of an erosion wave into the mountain range starting in the latest Miocene.