The soldier, who the military said was in civilian clothes and unarmed, was a student in a Jewish seminary in the West Bank that combines religious studies with service in the armed forces.
An Israeli military statement said the body was discovered near the settlement of Migdal Oz, north of the city of Hebron, and that the 19-year-old had been killed in a Palestinian attack.
There were no immediate claim of responsibility.
Hours later, Israeli Prime Minister Benjamin Netanyahu attended a previously scheduled ceremony in the West Bank settlement of Beit El and said Jews would not be driven from the area by Palestinians and that "we will deepen our roots in our homeland".
The Palestinians seek to end the Israeli occupation of territory seized in the 1967 Middle East and set up their own state in the West Bank, Gaza and East Jerusalem.