Up to 80,000 Hereros lived in Namibia when the uprising began. Afterwards, only 15,000 were left.
Over time, the skulls gathered dust in the German archives until three years ago when a German reporter uncovered them at the Medical History Museum of the Charite hospital in Berlin, and at Freiburg University in the southwest.
So far, 47 skulls have been found at the Charite and about a dozen more in Freiburg.
The publicity around their discovery prompted Herero and Nama leaders to ask the Namibian government to seek their return. After three years of talks, the delegation arrived in Berlin Sunday.
"The skulls will be handed over to the Namibian government in a ceremony that reflects their historical and cultural importance," a foreign ministry spokeswoman said, adding that Deputy Foreign Minister Cornelia Pieper would take part.
Charite spokeswoman Claudia Peter said the purported "research" on the skulls performed by German scientists had been rooted in the perverse racial theories that later planted the seeds for the Nazis' genocidal ideology.