“I am leaving this morning on a state visit to Germany, at the invitation of the President of Germany, Frank-Walter Steinmeier,” Herzog said in a statement.
“The main part of the visit will be the memorial marking the 50-year anniversary of the terrible massacre of the 11 Israeli athletes at the Munich Olympics in 1972,” he added.
The president’s trip to Munich follows a last-minute compensation deal reached last week between Germany and the families of the Israeli victims.
The bereaved relatives were offered $28 million by Berlin, in addition to $4.5 million previously granted.
Around 70 family members of victims are due to attend Monday’s memorial, Ankie Spitzer, whose husband Andre Spitzer was killed, told AFP.
The Israel Olympic Committee confirmed it would send a delegation to the September 5th memorial.
It will mark 50 years since gunmen from the Palestinian militant group Black September stormed the Israeli team’s lodgings.
They shot two people dead and took nine others hostage, all of whom were killed. Germany was blamed for botching an operation to rescue them.
Steinmeier’s office has not said whether the president will make a formal apology during the ceremony at Fuerstenfeldbruck air base, west of Munich, where the hostage-taking reached its violent end.
During his three-day visit to Germany, Herzog is also due to meet Chancellor Olaf Scholz and address parliament in Berlin.