Germany will ceremoniously return 20 skulls from the first recorded genocide of the 20th century.
An estimated 300 skulls were taken after a massacre of indigenous Namibians during an anti-colonial uprising.
German researchers used the skulls in Berlin for "scientific" experiments.
The goal is to encourage dialogue between the two countries and the descendants of the victims.
Germany will face up to a bloody chapter of its colonial past Friday when it hands back 20 skulls spirited away after what many historians call the first genocide of the 20th century.
A delegation of 55 Namibians is in Berlin to attend the solemn ceremony to receive the remains which they hope will be just a first step toward a greater reckoning with Germany's brief but brutal African adventure a century ago.
"We have come to first and foremost to receive the mortal human remains of our forefathers and mothers and to return them to the land of their ancestors," delegation member Ueriuka Festus Tjikuua told reporters in Berlin.
He said the mission intended to "extend a hand of friendship" to Germans and encourage a dialogue "with the full participation and involvement of the representatives of the descendants of those that suffered heavily under dreadful and atrocious German colonial rule".
The skulls are among an estimated 300 taken to Germany after a massacre of indigenous Namibians at the start of the last century during an anti-colonial uprising in what was then called South West Africa, which Berlin ruled from 1884 to 1915.
Incensed by German settlers stealing their land, cattle and women, the Herero people launched a revolt in January 1904 with warriors butchering 123 German civilians over several days. The Nama tribe joined the uprising in 1905.
The imperial German colonial rulers responded ruthlessly. General Lothar von Trotha signed a notorious extermination order against the Hereros.
Rounded up in prison camps, captured Namas and Hereros died from malnutrition and severe weather. Dozens were beheaded after their death and their skulls sent to German researchers in Berlin for "scientific" experiments.
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.
"They thought that they could prove that certain peoples were worth less than they were," she told AFP. "What these anthropologists did to these people was wrong and their descendants are still suffering for it."
German researchers have now determined the region from which the skulls came as well as the sex and age of the victims but say there is no hope of learning their identity or cause of death.
The Namibian representatives will return home Tuesday with a memorial service planned in the capital Windhoek the following day to welcome the 11 Nama and nine Herero skulls, which will go on display in a local museum.
The remains derived from four women, 15 men and a boy.
Ida Hoffmann, a former parliamentarian, said the delegation hoped to begin a dialogue with the German side that could eventually lead to direct reparation payments for the victims' descendants.
"I am here in Germany today to collect the remains of my ancestors. These skulls are but one part of human dignity. But the question remains: what of the other parts," she told reporters.
Germany has repeatedly refused reparations, saying that its 600 million euros ($818 million) in development aid since Namibia's independence in 1990 was "for the benefit of all Namibians".