Rania Siam was killed by either automatic gunfire or fragments of tank shells as she played outside her home on Friday, the sources added.
Two others were wounded in the incident, the sources said.
The death came shortly after a mortar attack by the Palestinian resistance group Hamas on a nearby Jewish colony in southern Gaza that wounded at least two Israelis, including a young child.
The girl was killed by gunfire that struck Khan Yunis in apparent retaliation for the earlier volley of mortars that hit the Gush Katif settlement bloc, Palestinian medics told agencies.
Aljazeera reports that the incident took place when Israeli forces fired randomly at Palestinian homes in the town.
'Splashed in blood'
An Israeli miltary source said soldiers had "returned fire towards the source of the mortar shell attack", adding that reports of the youngster's death were being investigated.
Palestinian children are getting
shot with troubling frequency
Rania Siam's death brought the overall death toll since the September 2000 start of al-Aqsa Intifada to 4607, including 3570 Palestinians and 963 Israelis, according to an AFP count.
Omar Siam, 50, the girl's father, recalled: "We were having lunch when suddenly there were some explosions and automatic gunfire.
"I felt a pain in my leg, but I was only lightly injured, thank God. Our meal was splashed in blood. We then realised that Rania had been killed by a bullet to the heat."
Omar Siam said his daughter was seven years old.
Friday's incidents followed an air strike that wounded a leader of the Popular Resistance Committees in southern Gaza a day earlier, in Israel's first assassination attempt since Yasir Arafat died in a Paris hospital on 11 November.
A second Israeli missile hit an explosives-laden truck in northern Gaza on Thursday night.