Isaac Herzog held talks in Ankara on Wednesday with Turkish counterpart Recep Tayyip Erdogan in the first visit by an Israeli president since 2007.
He then took part in a prayer for Ukrainian refugees as well as "Turkey and President Erdogan" with members of the Jewish community in Istanbul at the Neve Shalom synagogue in the historic Galata district.
"The entire process is without illusions, but reflects strategic and bilateral interests," Herzog told journalists about the visit and talks before entering the synagogue. He left Turkey shortly after.
"We will not agree on everything... But we shall aspire to solve our disagreements with mutual respect and goodwill," Herzog said during a press conference with Erdogan on Wednesday.
The Neve Shalom synagogue, which is also home to a museum about Jewish heritage, holds a special place for local Jews.
It is a synagogue which "suffered in the past", Herzog said, referring to terror attacks in 1986 which left 22 dead, and others in 1992 and 2003.
On November 15, 2003, 30 were killed and over 300 others were injured after vehicles filled with explosives targeted two synagogues in Istanbul.
The attacks were claimed by a Turkish cell of Al-Qaeda.
Under the Ottoman Empire, Istanbul, then Constantinople, welcomed many Jews expelled from Spain in 1492 who found refuge and established thriving communities until the 20th century.
In the 1930s, Jews were subject to discriminatory laws and pogroms.
These "500 years" of living together is often cited by Turkish officials, although the status of Turkish Jews has sometimes been less than equal.
Around 15,000 Jews live in Turkey today, the majority in Istanbul, compared with 200,000 at the start of the 20th century.