It was only the second Israeli operation there after two major campaigns in June and early July that killed at least 17 Palestinians and wounded 100 others.
The raid was carried out by “a large Israeli occupation army force estimated at more than 40 military vehicles, backed by a helicopter and drones”, Palestinian state news agency Wafa reported.
The Jenin Brigades armed group posted a photo of what it said was an Israeli drone that it had shot down.
Israeli security forces said the men detained belonged to Hamas and identified them as Ward Shuraim, Moatasem Jaaysa, and Abdullah Subh.
It said the men were “wanted for taking part in shooting attacks, IED attacks, rocket launches and the planning and advancing of additional terrorist attacks”.
Hamas, which controls the Gaza Strip and has fought several wars with Israel, confirmed that several of its members had been arrested, without naming them.
The father of Abdullah Subh told Palestinian state TV that his son had been wanted by Israeli forces.
“He's strong, stubborn and fierce. After high school, he was arrested for two years. Then he became wanted. There have been several attempts to take his life. In April, they [the Israeli army] fired at him. He still has a bullet in his back,” the father said.
Wafa reported that six people were injured by gunfire during the raid.
In July, Israel launched a major two-day campaign by land and air in one of the largest West Bank raids since the Second Intifada more than two decades ago.
The offensive came just weeks after a deadly Jenin raid on June 19 that included air strikes.
This year has been the deadliest on record since 2005, with more than 100 Palestinians killed, including children, and about 30 Israelis, the UN said.
Deadly operations by the Israeli army and attacks by Palestinian groups have become an almost daily occurrence in the occupied West Bank. On Friday, Israeli forces killed a 39-year-old Palestinian in the town of Aqaba.