Halima Uday Abu Samahdana took a bullet to the head when troops opened fire in the Shabura district of the impoverished town close to the Israeli-controlled border with Egypt, the medics and witnesses said on Saturday.
Witnesses said it was unclear why the Israeli troops had fired as there were no clashes underway at the time.
Aljazeera's correspondent in Gaza said the girl was at her home when she was shot.
An Israeli military source said he was unaware of the incident, but acknowledged that troops had opened fire elsewhere in Rafah.
Pregnant woman injured
Just hours later, two Palestinian women were also shot at and injured after Israeli occupation soldiers used live ammunition in northern Gaza's Bait Hanun.
Hospital director Mahmud al-Asali said one of the injured women - Latifa Abu Amsha - was shot at even though she is six months pregnant, and is now suffering internal bleeding and a broken leg.
Her mother, Jamila, said her 26-year-old daughter had been out to buy food and other essential supplies when the Israeli troops, who have reoccupied the town, opened fire.
"We were walking along when suddenly the army opened fire without warning," she told reporters, her clothes still soaked in her daughter's blood.
An Israeli military source insisted that the soldiers had first fired warning shots and added that they had helped with the women's evacuation to hospital.
The source added that the women had been wounded by shrapnel and not hit directly with Israeli bullets.