The rankings have also placed Makerere University College of Health Sciences in the second position on the continent.
Makerere University has been ranked the fifth best institution in Africa in the latest 2020 World University Rankings by the Times Higher Education.
According to the rankings released early this month, the university is also the best in East Africa, Central Africa, West Africa and Southern Africa.
The varsity's only rivals are institutions from South Africa.
The September rankings have also placed Makerere University College of Health Sciences in the second position on the continent.
On the global scene, the College of Health Science is in the 250th position.
"It is great to see Makerere University maintain her position among the top five universities in the continent in the prestigious 2020 rankings. Our medical school has also maintained its leadership as one of the top 250 medical schools globally and number two on the continent," Prof. Barnabas Nawangwe, the Vice-Chancellor of Makerere University said recently.
The Times Higher Education World University Rankings 2020 were released on September 11, revealing that in Africa, the University of Cape Town is the best while on the global scene, the University of Oxford leads.
The rankings consider research publications, education and general performance of the institution.
Last month, another university ranking scheme, Webometrics, had place Makerere University in position 16 in Africa, a rank scale, which was largely attributed, to increasing strikes at the Ivory Tower.
However, with strikes waning at the university, officials say, Makerere is now eyeing the first slot in Africa, in terms of research and education.
Top six in Africa
1. University of Cape Town (South Africa)
2. University of the Witwatersrand (SA)
3. Stellenbosch University (SA)
4. University of Kwazulu-Natal (SA)
5. Makerere University (Uganda)
6. American University in Cairo (Egypt)
Top five in the world
1. University of Oxford (UK)
2. California Institute of Technology (US)
3. University of Cambridge (UK)
4. Stanford University (UK)
5. Massachusetts Institute of Technology (US)