The official Palestinian news agency reported that “confrontations and violent clashes” erupted between residents of Jenin and the Israeli forces.
Old photos circulating on social media showed two of the three Palestinians who were killed posing with rifles. Palestinian media also shared footage showing an ambulance hit by Israeli gunshots in Jenin.
Palestinian factions in the city called for a general strike to mourn the dead and show solidarity with their families.
On Wednesday, Israeli soldiers shot and killed a Palestinian militant who opened fire at them near the West Bank settlement of Ofra.
More than 140 Palestinians have been killed in Israeli-Palestinian fighting in the West Bank and east Jerusalem this year, making it the deadliest year since 2006.
The Israeli army says most of the Palestinians killed have been militants. But stone-throwing youths protesting Israeli army incursions and others not involved in confrontations have also been killed.
Israel has been conducting daily arrest raids throughout the West Bank, in an operation prompted by a spate of Palestinian attacks against Israelis in the spring that killed 19 people.
The military says the raids are meant to dismantle militant networks and thwart future attacks, but the Palestinians say they entrench Israel’s open-ended occupation, now in its 56th year.
At least 31 people have died in Arab attacks in Israel and the occupied West Bank this year, according to Israeli figures.