The army said soldiers had fired warning shots before opening fire on a group throwing stones at Israeli civilians.
Palestinian security officials said the stones had been thrown at military vehicles.
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The teenager was killed near the Tapuah settlement, south of Nablus, and a 19-year-old was wounded in the same incident, they added.
Around 20 Palestinians have been killed by the army in the West Bank since June, according to an AFP tally.