Israeli rights group HaMoked said the 14-year-old girl, named only as Ghada, was arrested in Jerusalem on January 13 without a permit while visiting the Israeli-controlled city.
While she is from a-Ram a few kilometres (miles) north of Jerusalem, her father is originally from Gaza, the Palestinian territory about 80 kilometres away that is hermetically sealed off by Israel.
HaMoked said the girl was told she would be dropped off at a checkpoint near her home but on her release on January 16 instead was taken to the Erez crossing into Gaza.
She said Ghada had never been in Gaza before and did not know anyone there, though she was now staying with members of her extended family.
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"No one told her anything -- they told her they would send her to Qalandia (checkpoint near her home) but they sent her to Erez."
She said Ghada has epilepsy and was concerned the stress could affect her condition.
A spokesman for the Israel Prison Service said they were examining the case, stressing however that according to official records the girl was a Gaza resident.
Joubran-Dakwar said it was the first time she had heard of someone as young as 14 being sent there.
Israel has maintained a blockade on Gaza for more than a decade which it says is necessary to isolate the strip's Islamist rulers Hamas, with whom it has fought three wars.
It is extremely difficult for Palestinians from the West Bank to obtain Israeli permission to visit the strip.