Ahmed Daqamseh had killed the eighth graders in a 1997 shooting rampage at the scenic "Island of Peace" border post where he was stationed. Seven other girls were wounded at the time.
The release could raise tensions between Israel and Jordan. In 2011, Israel summoned Jordan's ambassador to express anger after the kingdom's justice minister at the time called for Daqamseh's release.
Amer Sartawi, a spokesman for Jordan's Public Security Directorate, said Daqamseh was freed early today.
After the shooting, Jordan's King Hussein - the late father of the current king, Abdullah II - rushed to Israel and paid condolence visits to the girls' families, a gesture that touched many Israelis at the time.
The shooting came three years after Israel and Jordan signed a peace treaty.
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