We present a new stratigraphy of the Jianchuan basin, one of the largest Cenozoic sedimentary basins in southeastern Tibet. This basin was regarded as recording sedimentation from the Eocene up to the Pliocene, and as such has been the focus of several studies aiming at constraining the environmental, tectonic and topographic evolution of the area. Within the Shuanghe and Jianchuan formations thirteen new zircon U/Pb ages and one biotite 40Ar/39Ar age of interbedded and cross-cutting ultrapotassic magmatic rocks show that a brief magmatic event occurred from ~ 35.7 to ~ 34.5 Ma (35.2 ± 0.4 Ma on average). The uppermost formation (Jianchuan Fm), supposedly Pliocene in age, is related to this magmatic event and is 35.4 ± 0.8 Ma old. All sedimentary formations are thus Eocene in age, with neither Oligocene nor Miocene sediments. The coal-bearing Shuanghe Formation yields a fossil of a large amynodontid typical of the Upper Eocene Ergilian interval (37.2 to 33.9 Ma). Sedimentation of the Shuanghe Formation took place in a short time interval at ~ 35.9 ± 0.9 Ma, after a large-scale drainage reorganization that induced the abandonment of a large braided-river system. This reorganization was possibly linked with the initiation of the left-lateral Ailao-Shan Red River fault and/or to widespread magmatism in the Jianchuan basin. Previous high paleoaltitude estimates for the Jianchuan basin are thoroughly re-evaluated and yield a value of 1200 ± 1200 m.a.s.l. for the Upper Eocene.