A police statement said the 19-year-old approached officers at the Tapuah junction, ignored orders to stop and pulled a knife.
"At this point the officers shot her," police said, adding that she was killed.
Police identified her as a resident of Asira Al-Shimaliya, a village north of Nablus, which is located near the Tapuah junction.
Also known as Zaatara junction, it has been the site of a number of violent incidents.
The Palestinian health ministry said "a woman was killed after being shot by the occupation forces at Zaatara checkpoint."
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Violence since October 2015 has killed 234 Palestinians, 36 Israelis, two Americans, one Jordanian, an Eritrean and a Sudanese national, according to an AFP count.
Most of the Palestinians killed were carrying out attacks, according to Israeli authorities.
Others were shot dead during protests or clashes, while some were killed in Israeli air strikes on the Gaza Strip.