The Mombasa-Nairobi SGR generally runs parallel to the Uganda Railway, a metre-gauge line that was built during British colonial rule.^[14] The SGR, however, has a straighter alignment that accommodates higher speeds. Because of the rough and hilly terrain, large portions of the SGR were built on viaducts and embankments and in cuttings.

For example, the Uganda Railway tackled the hilly terrain near Mazeras township by using a spiral. In contrast, the SGR passes through this area on two bridges, with the 43.5 metres (142 ft 9 in) high Mazeras-2 bridge being the highest one on the route. As it approaches Nairobi, the SGR crosses the 2.6 kilometres (1.6 mi) Athi River Super Bridge, which at the time of its completion was the sixth-longest bridge in Africa. The SGR has a total of 98 bridges.^[15]