Peres, who was accompanied by survivors of Nazi death camps, will also hold talks with Chancellor Angela Merkel and his German counterpart Horst Köhler, his spokesman said in a statement.
The president emerged from his plane wearing a long, dark coat against the freezing Berlin weather and was received with full military pomp and ceremony, including a guard of honour and a 21-gun salute.
"The trip marks the completion of a personal circle for the president, whose own grandparents and uncle were burned alive in the Vishneva synagogue," his spokeswoman Ayelet Frish said, referring to a town in modern-day Belarus.
The president's speech on January 27, the International Holocaust Remembrance Day, "will mourn the six million Jewish lives that perished in the Holocaust including those of his grandparents and his uncle," Frish said.
The speech, in Hebrew, will conclude with "his vision and hope for the future of Israel, Germany and the Middle East."
In what is likely to be an emotional visit, Peres will also hold a memorial service at platform 17 of the Grunewald train station from where Berlin's Jews were expelled to Nazi labour and death camps.
Peres' trip comes exactly one week after Prime Minister Benjamin Netanyahu visited Berlin for a meeting between the German and Israeli cabinets dominated by the Middle East peace process and the Iranian nuclear programme.
Netanyahu was also due to attend Wednesday's anniversary ceremony marking the liberation of Auschwitz by Soviet troops.
On Thursday, Peres is due to leave Germany for Davos in Switzerland where he will join world leaders and top officials at the World Economic Forum.