The unexpected trip to the Bavarian city of Regensburg was described as “a private visit” made necessary by the deteriorating health of Benedict's 96-year-old brother Georg Ratzinger, said Clemens Neck, a spokesman for the Regensburg bishopric.
“It might be the last time the brothers see each other in this world,” Neck told AFP.
The Vatican confirmed the trip and said the only other time 93-year-old Benedict had left the Vatican since his resignation was a visit to the Castel Gandolfo papal palace outside Rome.
It is believed to be his first time back in Germany since 2011.
Benedict, seen as a traditionalist in the Catholic Church, stunned the world when he became the first pope in 600 years to resign, citing health reasons.
The former pontiff, whose original name is Joseph Ratzinger, now lives in a small former monastery inside the Vatican and has largely stayed out of the public eye.
“I wish Pope Emeritus Benedict XVI a good stay in Germany and the necessary rest to privately look after his brother,” Georg Baetzing, the head of the German Bishops' Conference, said in a statement.
The trip comes just days after numerous EU countries reopened their borders to Europeans as coronavirus lockdowns are eased..
Given his own frail health, Benedict was travelling with a doctor and a nurse, Vatican spokesman Matteo Bruni told reporters in Rome.
He will stay in Regensburg as long as necessary, Bruni added.
The two siblings have a “firm” bond, according to the official Vatican News site, which said that Georg had made regular trips to Rome to see his brother over the years.
Both were ordained priests on the same day in June 1951, it added.
Georg Ratzinger went on to conduct the thousand-year-old Regensburg cathedral choir, known as the Regensburger Domspatzen.
But the renowned choir fell under the shadow of the Catholic Church's child abuse scandal after a 2017 report found that more than 500 choir boys suffered sexual or physical abuse at the institute from 1945 to the early 1990s.
The report criticised senior Church figures for failing to do enough to prevent the abuse, including Georg Ratzinger who led the choir from 1964 to 1994.
Ratzinger has said he knew nothing about the violence at the school.