The military 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.
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 were seen assessing the damage, as ambulance sirens blared in the background.
The Palestinian Red Crescent ambulance service said at least one Palestinian was killed and three others were injured. It had earlier said that two people were killed.
Residents of the camp said they received warnings from the Israeli military to stay away from the militants due to an impending incursion into the camp. They said the military did not specify a date.