Independent details about the killing are as yet unavailable.
However, an Israeli military official said "a suspect Palestinian was seen approaching the security fence around the base. The soldiers tried to stop him by firing warning shots and then fired in his direction" at the Ofra military base.
The official added: "The Palestinian was not armed. The soldiers gave him first aid but he died of his injuries."
The latest death brought the overall toll since the September 2000 start of the Palestinian uprising to 4595, including 3559 Palestinians and 962 Israelis.
Rocket launcher destroyed
In a separate incident, the Israeli air force said they destroyed a rocket launcher in the northern Gaza Strip as Palestinian resistance fighters were about to launch an attack.
"A group of Palestinians were spotted in Bait Hanun as they were about to fire a Qassam rocket on Israel's territory. The rocket launcher was destroyed and the Palestinians fled the scene," a military source said.
The number of unarmed civilians
killed by Israeli troops is rising
The crude rockets are manufactured by Islamic resistance group Hamas and named after its military wing - the Izz al-Din al-Qassam Brigades.
However, Hamas has not yet confirmed that its fighters were involved in the incident.
Six Israelis have been killed in rocket attacks in the past few months.