The fossil was unearthed at the site of an extinct volcano in the country's remote northeast Karamoja region, one of the least developed areas in Uganda, the BBC reported Tuesday.
Researchers say the skull of the ancient tree-climbing herbivore is about the same size as that of a chimpanzee, but its brain was smaller.
Martin Pickford, a palaeontologist from the College de France in Paris, and Brigitte Senut of the French National Museum of Natural History said the skull was from a creature they've dubbed Ugandapithecus major.
"It is a highly important fossil and it will certainly put Uganda on the map in terms of the scientific world," Pickford said.
Senut said the remains would be transported to Paris to be X-rayed and documented and then returned to Uganda.
"It will be cleaned in France, it will be prepared in France... and then in about one year's time it will be returned to the country," she said.