The limestone figurine believed to be of Ankhesamon was among hundreds of artifacts taken from the museum in Mallawi, amid looting and civil unrest following the overthrow of President Mohammed Morsi.
It was traced by police to a coffee shop owner in the Khan el-Khalili bazaar district of the capital, Cairo.
A senior official told BBC the statue was largely in a good condition.
It needed some restoration work, but would go on display in a new museum devoted to the family of Tutankhamen’s father, the Pharaoh Akhenaton, said Ahmed Sharaf, head of Egypt’s museum department.
The family of Akhenaton, who ruled ancient Egypt around 1,500 B.C., would now be reunited, said Sharaf.
The Mallawi museum was one of several ransacked across the country during the riots that broke out as the security forces cracked down on Islamist supporters of Morsi who were staging a sit-in in Cairo.
Antiquities Minister Mohamed Ibrahim said the 13-inch statue of the girl was “one of the most important in the museum”.
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Ibrahim told the AFP news agency that about 1,050 artifacts had been stolen at that time, of which about 800 had been recovered.
Egypt’s ancient sites have been targeted by treasure-seekers for centuries, with the tomb of the boy pharaoh Tutankhamen famously surviving almost intact.
But the BBC’s Arab Affairs editor Sebastian Usher says the upheavals in Egypt since the overthrow of Hosni Mubarak in 2011 have helped looters target museums and archaeological sites for ancient treasures to sell on the black market.