Significant late Cenozoic uplift (>1000 m) of the northern half of the Sierra Nevada (California, USA), a mountain range in the North American Cordillera, has been a dominant paradigm over the past century. This paradigm has been supported by evidence suggesting that in response to this recent uplift, the range’s deep canyons were incised in the past 3–4 m.y. However, paleochannel elevations compiled from a mining report and geological maps demonstrate that while some modern rivers have incised 560 m below their Eocene–early Oligocene riverbeds, incision by others has been <300 m. For example, Eocene–early Oligocene fluvial gravels can be found just 161 m above the modern channel deep within the canyon of the South Fork American River. We conclude that the initiation of late Cenozoic incision was due to a resumption of a period of downcutting that was interrupted in the Eocene when the rivers were buried by fluvial sediment and by later volcanic deposits. This interpretation challenges the hypothesis that recent uplift was responsible for deep canyon incision. Correctly identifying the causes of recent incision in the northern Sierra Nevada has important implications for understanding the geological history of the North American Cordillera because the range is hypothesized to have been the western ramp of the Nevadaplano.