Suez rift is one of the active seismic zones in the northward continuation of the Red Sea, as indicated by recent earthquake records from the Egyptian National Seismological Network (ENSN). We present a new model of P and S wave velocities in the crust and uppermost mantle beneath the Gulf of Suez and surrounding areas, including the northern portion of the Red Sea. Using the records from 94 seismic stations, we analyzed ~ 66,000 P and ~ 17,000 S wave arrival times from 9700 events. The travel time tomography inversion was performed using the iterative LOTOS code. The spatial resolutions of the derived models were assessed using several synthetic tests. The most prominent anomaly is a sharp high-velocity anomaly beneath the Red Sea, which is observed in both the P and S models at all depth intervals. We interpret this anomaly to be oceanic crust that was formed through extension associated with a dispersed system of spreading centers. Beneath the Gulf of Suez, the upper and middle crusts appear to be strongly heterogeneous and are dominated by low-velocity anomalies, indicative of the continental nature of the crusts. In contrast, at a depth of 30 km, we observe a prominent high-velocity anomaly along Gulf of Suez, which is interpreted to be the result of crustal thinning associated with extension between the Sinai block and the African Plate. The thickness of the crust beneath the rift is estimated to be approximately 25 km, whereas that in the surrounding areas appears to be 30–35 km. In the northwestern part of the area, we observe a low-velocity zone in the middle and lower crusts that coincide with intense seismicity and a well-developed system of recent faults on the surface. This region may mark a possible area of northward propagation of the Suez Rift zone.