Police spokeswoman Luba Samri said that the suspect walked down a passage for vehicles, “waving a knife in his hand,” adding that he approached a security guard at the checkpoint before other guards shot him.
A separate notice confirmed his death without disclosing details about his identity.
The checkpoint, located east of Jerusalem, was closed off following the shooting.
It was the first such incident in two weeks.
A year-long wave of violence in the West Bank and Israel has killed at least 230 Palestinians and 34 Israelis since September 2015.
Israel says that most of the Palestinians were killed for perpetrating or attempting to carry out stabbing, car-ramming and shooting attacks.
The Palestinians and human rights organizations say that Israel is using excessive forces to quell the uprising, and in many cases, kill Palestinians who could be stopped without using lethal force or were mistaken to be attackers.
Israeli leaders accuse the Palestinian National Authority of “inciting” the unrest, while the Palestinians say it is the result of nearly 50 years of Israeli occupation of the West Bank and the Gaza Strip, home to more than five million Palestinians, where they wish to establish their state. Enditem