The move took place as Israel was to begin marking memorial day for fallen soldiers and the victims of terror attacks, which begins at sundown.
Mohammed Abu Khder, 16, was kidnapped from annexed east Jerusalem on July 2 and his burned body was found hours later in a forest in the western part of the city.
Although a number of Arab names are featured on the wall, it is the first time the name of a Palestinian killed by Jewish Israelis has been listed.
The vast majority of the names are of Jewish Israelis killed in attacks carried out by Palestinian militants.
Abu Khder was allegedly killed by three Jewish extremists in revenge weeks after the kidnap and murder of three Israeli teenagers by Palestinian militants in the southern West Bank.
Speaking to AFP, his father, Hussein Abu Khder, said he had not been informed of the decision to list his son's name on the memorial.
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"I am Palestinian, not Israeli, even if I am a resident of east Jerusalem, and I do not want his name written next to that of Israeli soldiers," he said.
"What I expect of Israel is justice and that my son's killers be jailed for life."
The three suspects are currently on trial at a court in Jerusalem.
Abu Khder's name had already been added to the official list of terror victims in July.
The wall, which bears 2,538 names, is located at the national cemetery on Mount Herzl in Jerusalem.
It is also the location of Israel's main military cemetery and the place where the main remembrance ceremonies will take place on Wednesday.