Muhammad Fahmi Krakara, described 14 or 15 years old, died while sitting in his father's truck, as his father completed maintenance work on the border fence on behalf of the Israeli Defense Ministry.
An anti-tank projectile fired from Syria struck, killing the boy and injuring the father and two other workers at the fence.
It wasn't clear if the projectile came from Syrian troops or rebels, but Israeli officials determined it was intentional.
"Today's event on the Syria border intentionally targeted Israelis," the Israel military Twitter account said. "The explosion is the most serious attack against Israel in recent months."
The Israeli military responded with tank fire.
The death was the first at the northern Israeli border since December when Sgt. 1st Class Shlomi Cohen was fatally shot by a Lebanese soldier.