Gauck is the first German leader to visit Oradour-sur-Glane, where ruins from the war have been preserved as a memorial to the dead. They include a church where women and children were locked in, before toxic gas was released and the building set on fire.
Some 205 children aged under 15 were among victims of the June 10, 1944 atrocity which left deep scars in France.
After the war, French General Charles de Gaulle, who later became president, decided that the village should not be rebuilt but remain a memorial to the barbarity of Nazi occupation. A new village was built nearby.
In 1999, French president Jacques Chirac dedicated a memorial museum which includes items recovered from what became known as the 'Village of Martyrs'.
They include watches stopped at the time the owners were burnt alive, glasses melted from intense heat and other personal items.
Wednesday's highly symbolic visit follows a 1984 commemoration when then French president Francois Mitterrand and former German chancellor Helmut Kohl attended a memorial service for fallen soldiers at Verdun.
The Battle of Verdun (February-December 1916) claimed the lives of more than 700,000 soldiers and came to symbolize the horror of war for both the Germans and the French.
As they stood in front of the Douaumont Ossuary, which contains the remains of 130,000 fallen soldiers, Mitterrand and Kohl joined hands – a gesture of friendship marking the lessons learned from a frightful past.
But the scars run deep in Oradour where an association of families of the martyrs had thus far opposed any visit by a German leader.
The two presidents are due to visit the village square where the residents were rounded up by German soldiers ostensibly to have their identity papers checked. The women and children were then locked up in the church while the men were taken to a barn where machine guns awaited.
The two presidents will be accompanied by two of the three living survivors — Robert Hebras, 88 and Jean-Marcel Darthout.
Hebras, who was 19 at the time of the massacre, survived as he was buried under the corpses of others who were machine-gunned.
"I was consumed by hatred and vengeance for a long time," he said, adding that Gauck's visit came at an opportune time.
"Any earlier would have been too soon," he said, adding: "We must reconcile with the Germans."
Germany in 2010 reopened a war crimes case into the attack when a historian discovered documents implicating six suspects in their 80s.
The suspects, aged 18 and 19 at the time, allegedly ordered the inhabitants to assemble in the village square.
Prosecutors eventually identified 12 members of the regiment who were still alive after trawling through files of the Stasi secret police in the former communist East that came to light after German reunification in 1990.
"A case has been opened against seven of them," Ulrich Schepers, of the public prosecutor's office in the western city of Dortmund, told AFP. The other five have already served sentences in France.
German prosecutors travelled to Oradour and Bordeaux in January and took witness statements from 11 survivors, consulted archives and questioned three French former soldiers involved.
They expect a decision on whether a case will go to court from as early as the end of this year.
Gauck, a former East German human rights activist, has already paid two visits to the sites of Nazi mass killings in Europe; the Czech village of Lidice near Prague in 2012 and the Italian hamlet of Sant'Anna di Stazzema in March this year.