The Great Rift Valley is part of an intra-continental ridge system that runs through Kenya from north to south. It is part of the Gregory Rift, the eastern branch of the East African Rift, which starts in Tanzania to the south and continues northward into Ethiopia. It was formed on the "Kenyan Dome" a geographical upwelling created by the interactions of three major tectonics: the Arabian, Nubian, and Somalian plates. In the past, it was seen as part of a "Great Rift Valley" that ran from Madagascar to Syria. Most of the valley falls within the former Rift Valley Province.

The Gregory Rift is the eastern branch of the East African Rift fracture system. The rift is being caused by the separation of the Somali plate from the Nubian plate, driven by a thermal plume. Although the term is sometimes used in the narrow sense of the Kenyan Rift, the larger definition of the Gregory Rift is the set of faults and grabens extending southward from the Gulf of Aden through Ethiopia and Kenya into Northern Tanzania, passing over the local uplifts of the Ethiopian and Kenyan domes. Ancient fossils of early hominins, the ancestors of humans, have been found in the southern part of the Gregory Rift.