Rawan Abu Zaid was shot twice in the head in her home in Rafah's Brazil neighbourhood on Saturday, according to the head of Rafah's main hospital.
The girl's family said she was hit by Israeli army fire as she walked to a shop.
A total of 43 Palestinians have been killed in Rafah since the start of Israel's Operation Rainbow, launched to round up wanted Palestinian activists and stamp out weapons smuggling under the border with Egypt.
Aljazeera's correspondent reports that Israeli occupation forces and tanks have partially withdrawn from the area. However, they are still positioned in parts of the town, including near the girl's home.
More than 1000 Palestinians have also been left homeless after the Israeli occupation army demolished more than 100 homes in the area, according to figures released by a United Nations agency.
The offensive has drawn a hail of international criticism, including a rare rebuke from the US and censure from the United Nations.
At least four people, including an Israeli occupation soldier have been injured after a Palestinian blew himself up at a checkpoint near the West Bank city of Nablus.
The suspicious behavior of the bomber, who was wearing an explosives-packed belt, drew the attention of Israeli soldiers who fired warning shots in the air to stop him as he approached the checkpoint from the east, according to reports.
More than 100 homes were
demolished in Rafah last week
The bomber then detonated the explosives, about 30m away from the checkpoint, wounding the soldier and three Palestinians, one of them seriously. Paramedics said the bomber was killed in the attack.
There was no immediate claim of responsibility.
The blast went off near the Bekaot checkpoint close to the Tamun village in the northern Jordan Valley, east of Nablus.
Palestinian medical sources also said an 18-year-old Palestinian died early on Saturday from wounds he received from Israeli gunfire during a raid in Gaza City on 12 May.
Husayn al-Lada was seriously wounded during the invasion in the city's al-Zaitun neighbourhood in which nine other Palestinians, including a child, were killed.
Also on Saturday, clashes erupted between citizens of Nablus city and Israeli occupation forces when an Israeli special unit raided the city in the early hours of the morning, Aljazeera's correspondent reported.
Israeli forces have also raided Qalqilya city and arrested one Palestinian. This brings to 18 the number of Palestinians detained in the past few days, including Hamas activists, the correspondent added.