The University of Glasgow's earliest connection with Kenya was through alumnus, Thomas Watson, who joined the East Africa Scottish Mission, founded in 1889, and helped establish stations in Kenya, laying the earliest educational as well as Presbyterian foundations through his missionary work.

It was during the twentieth century that the University began what was to become a long history of supporting veterinary and human medical training in East Africa, with the first move to develop veterinary education there in the 1920s. Teaching links were decisively strengthened in the 1960s as the East African countries gained their independence.

In 1962, Sir Thomas Symington, St Mungo Notman Chair of Pathology at the University of Glasgow, went as part of a working group to East Africa to look at the medical needs of Uganda, Kenya and Tanzania. The University of East Africa consequently came into existence in 1963 as a federal university to serve the newly independent countries, and was made up of three colleges: Makerere University College in Kampala, University College in Nairobi, and University College in Dar-es-Salaam.

Symington himself was instrumental in the establishment of the new medical schools in Nairobi and Dar es Salaam, and encouraged secondments of staff from Glasgow to these schools as well as the further training of young African graduates in Glasgow. Notable staff who went to Kenya on secondment included: Ian McIntyre, the first Professor of Veterinary Medicine at the University of Glasgow (1961 to 1983), who was seconded to the University of East Africa, University College, Nairobi as Dean of the Faculty of Veterinary Science and Professor of Clinical Studies from 1963 to 1967, helping to develop existing training courses to University Degree standards.

The Glasgow graduate and eminent pathologist, Bill Jarrett, also spend a period in Kenya from 1963 as part of the Glasgow contribution to an international team to establish the Veterinary School of the University of East Africa in Nairobi. During this time he carried out major research into the cause of East Coast Fever in cattle, which would form the basis of subsequent vaccine development in Africa. In turn, Jarrett’s experience in Nairobi also influenced his input in Glasgow Veterinary School’s subsequent innovative undergraduate curriculum, which is now commonplace in veterinary education worldwide.

The University of East Africa, in an attempt to support the well-established, but over-subscribed Makerere Medical School at Kampala, Uganda, invited the collaboration with the University of Glasgow to establish a medical teaching centre in Nairobi with the hope of producing more doctors to meet the demand in the East African regions. Similar to the Veterinary School, this collaboration saw University teachers as well as hospital staff from Glasgow seconded to Nairobi to develop a complete medical curriculum, and young East African doctors were seconded to Glasgow for further training so as to return as teachers and researchers. Full medical courses in Nairobi started on 1 July 1967.

In 1970 the University of East Africa was split into three independent universities. The University of Nairobi’s School of Medicine offers every level of academic study in Medicine and is the only university in Kenya to offer a degree in Bachelor of Veterinary Medicine.

University alumni were also instrumental in the mapping of Kenya; Professor of Geology from 1904 to 1929, John Walter Gregory produced "The Great Rift Valley" (1896) based on his scientific expeditions in East Africa, and had the 'Gregory Rift' named for him, which runs through Kenya. Kenya-born geologist Lawrence Williams BSc 1952, was member of the Geological Survey of Kenya and lectured at the University in Nairobi.