Makerere's world ranking also improved from 4,836 to 3,811 in the six months since the last ranking.
When the grading was first published in 2004, Makerere was 18th on the continent, but slipped to 23rd in 2005 and 24th in 2006.
At 16th place, Strathmore University (Kenya) is the best ranked institution in East Africa while University of Dar es Salaam is in 25th place. Other universities in the region to find a place on the list are Egerton University (29), University of Nairobi (54), Moi University (83) and Kenyatta University (100). The best seven African universities are from South Africa.
Academics at the country's top institution of higher learning say the improvement is a reward for the improvement in research among students and lecturers.
"Our improvement in ranking has been as a result of more programmes introduced at the institution and introduction of a research and intellectual property rights policy," Dr Williams Ddembe, the deputy dean of the Faculty of Computing and IT said.
He also attributed the improved ranking to a curriculum review and said the institution is committed to further improving the ranking.
At 58th, Kampala International University (KIU) is the only other Ugandan institution to make it to the top 100 in Africa.
Makerere's Faculty of Computing and Information Technology was also rated independently as the 56th in Africa. The rankings are an initiative of Cybermetrics Lab, a research group of the Centro de Information Documentation, the largest public research body in Spain.