We investigate the upper-crustal structure of the Rukwa-Tanganyika Rift Zone, East Africa, where earthquakes anomalously cluster at the northwestern tip of the Rukwa Rift, the eastern tip of the Mweru-Wantipa Rift, and along the Tanganyika Rift axis. The current rift tips host distributed faulting in exposed basement with little sedimentation. Here, we invert earthquake P and S travel times to produce three-dimensional upper-crustal velocity models for the region. The resulting models reveal the occurrence of anomalously high Vp/Vs ratios that extend from the surface down to ca. 10 km at the tip zones of the Rukwa and Mweru-Wantipa rifts. The spatial association of distributed faulting, upper-crustal seismicity, and thermal anomalies with the high Vp/Vs ratios suggest a weakened crust below the rift tips’ flexural zone. We propose an ongoing strain localization and crustal softening at the rift tips that is accommodated by brittle damage from bending strain, and potentially compounded by hydrothermal weakening. This setting represents a precursory phase that may initiate unilateral rift tip propagation.