This may have been because the supreme leader was still using an underground bunker below the compound for his protection (though not reportedly some of the deepest that the regime has).
Multiple munitions may have been needed to burrow deep enough to be sure of striking the target.
Other sites in the Iranian capital were also hit, including the office of President Masoud Pezeshkian who later put out a statement and said he was safe.
Three senior Iranian defence officials have been confirmed dead by Iran, including Defence Council secretary Ali Shamkhani, Defence Minister Brig Gen Aziz Nasirzadeh and IRGC commander Gen Mohammad Pakpour.
When the jets stuck, it was the middle of night at Mar-a-Lago in Florida where President Trump had gathered along with some of his top officials to monitor events.
It would take hours before confirmation came that the supreme leader had been killed.
Iran had been prepared for this possibility though, with reports that the plans for succession for not just Khamenei, but also an array of senior officials had been put in place.
That means it is not yet clear what the killing will mean for the course of this conflict.