•New high-resolution magnetostratigraphic study constrains the Gonjo Basin from 69 to 41.5 Ma.•Rapid SR and rotation periods suggest pulses of Tibetan crustal shortening at 69-67 Ma and 52-48 Ma.•Tibetan crustal shortening pulses correlate with India-Asia convergence rate. Models that aim to explain the causes of the significant Indian plate motion acceleration around 70 Ma, and the subsequent deceleration around 52 Ma predict different scenarios regarding crustal shortening of the Tibetan Plateau, which can be tested by precisely determining the timing of regional shortening events in Tibet. Here we attempt to determine this timing by presenting a high-resolution magnetostratigraphy of a ∼3.5 km thick sedimentary sequence in the syn-contractional Gonjo Basin, east-central Tibet. We successfully isolated the primary remanence as confirmed by positive fold and reversal tests. Correlation to the geomagnetic polarity time scale reveals a 69–41.5 Ma age for the Gonjo Basin sedimentary succession. Average sedimentation rates indicate two episodes of enhanced sediment accumulation rate at 69–64 Ma and 52–48 Ma, which coincide with periods of vertical axis rotation recorded in the basin fill. This coincidence suggests a tectonic cause, which given regional structures we interpret as shortening pulses. Our results are similar to those from basins elsewhere in southern, central and northern Tibet, suggesting plateau-wide, synchronous shortening pulses at ∼69–64 Ma and ∼52–48 Ma. These pulses are synchronous with major acceleration and deceleration of India-Asia convergence rate, suggesting that both the acceleration and deceleration of India-Asia convergence may be associated with enhanced crustal deformation in Tibet, which we use to evaluate previous dynamic models explaining the Indian plate motion changes and India-Asia collision processes.