The IDF said the site was used by members of Hamas and Islamic Jihad movements.
"In a joint IDF and ISA [Israel Securities Authority] activity, the IDF conducted an aerial strike on an underground terror compound in the Al-Ansar mosque in Jenin," the IDF said on Telegram.
"The mosque contained a terror cell of Hamas and Islamic Jihad terror operatives who were organizing an imminent terror attack," it added.
The mosque was used "by the terrorists as a command center to plan the attacks and as a base for their execution."