A second girl was also injured in the attack at the school in the Berlin district of Neukölln, they said.
The schoolmates, aged between seven and eight, were both rushed to hospital.
A suspect was arrested close to the school grounds following the incident.
The circumstances surrounding the attack were not immediately clear, a police spokeswoman said.
Neither was it clear whether the assailant was known to the schoolgirls, the spokeswoman said.
Berlin’s regional interior minister Iris Spranger said she was “deeply shocked” by the events at the school, confirming the girls had been attacked with a knife.
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