The Israeli military said it blasted a “terrorist route” under the al-Ansar Mosque in Jenin refugee camp that it said was being used by militants to organise attacks.
Palestinian medics said at least one person died in the strike.
It is at least the second airstrike in recent days to hit the West Bank, where violence has surged since Hamas gunmen from Gaza carried out a deadly October 7 rampage in Israel.
The Israeli military said in a statement: “Intel was recently received which indicated that the terrorists, (who) were neutralised, were organising an imminent terror attack.”
The IDF released images that it said showed an entrance to a bunker under the mosque.
It also released a diagram that it said showed where militants had stored weapons there.
In a tweet, the IDF wrote: “The IDF & ISA just conducted an aerial strike on a Hamas and Islamic Jihad terrorist compound in the Al-Ansar Mosque in Jenin.
“Recent IDF intel revealed that the Mosque was used as a command centre to plan and execute terrorist attacks against civilians.”
Jenin refugee camp, a Palestinian militant stronghold, was the focus of a major Israeli military operation earlier this year.
Footage on social media, appearing to show the scene of the air strike, showed a gaping hole in one of the mosque’s exterior walls, surrounded by debris.
Several dozen Palestinians are seen assessing the damage, as ambulance sirens blare in the background.
The Palestinian Red Crescent ambulance service said at least one Palestinian was killed and three others injured. It had earlier said that two people were killed.
The Israeli Air Force said: “In a joint IDF and ISA activity, the IDF conducted an aerial strike on an underground terror compound in the Al-Ansar mosque in Jenin.
“The mosque contained a terror cell of Hamas and Islamic Jihad terror operatives who were organising an imminent terror attack.
“The terrorist cell also carried out a terror attack on October 14th in the area of the security fence, where an explosive device was detonated by a cellular activation of terror forces who arrived at the scene.”
It comes after Israel last night vowed to ramp up airstrikes on Gaza as it prepares for the “next stage of war”.
The IDF said bombing raids will be crucial in “minimising danger” to create the “best conditions” for invasion.
Tens of thousands of troops and huge columns of tanks remain massed on the Israel-Gaza border awaiting orders.
Speaking at a press conference on Saturday night, IDF spokesperson Daniel Hagari said: “We have to enter the next phase of the war in the best conditions, not according to what anyone tells us.
“From today, we are increasing the strikes and minimising the danger.”