All praise is due to Allah, and peace and blessings be upon our master, the Messenger of Allah ﷺ.
Facing the actual structure of the Ka‘bah (‘ayn al-Ka‘bah) is one of the conditions for the validity of the prayer. The scholars have clarified what is meant by "the actual structure of the Ka‘bah."
Imam ash-Sharwānī (raḥimahullāh) said: "What is meant by its ‘ayn (actual structure) is its physical body, or the airspace directly aligned with it — if the person praying is not inside it. But if he is inside it, then the airspace alone does not suffice; rather, the actual physical structure must be faced, such that even if he faces a projecting part of it measuring roughly two-thirds of a dhirā‘ (cubit) or more, this would be sufficient." [Ḥāshiyat ash-Sharwānī ‘alā Tuḥfat al-Muḥtāj, Vol.1/P.484]
Sheikh al-Qulyūbī (raḥimahullāh) said: "Unlike one who prays outside it — i.e., outside the Ka‘bah — for him the airspace (directly above it) suffices, even if he is higher than it, or even if he is at the location where it (hypothetically) has been demolished." [Ḥāshiyat al-Qulyūbī ‘alā Sharḥ al-Minhāj, Vol.1/P.154]
Accordingly, the prayer is valid on the upper floors of al-Masjid al-Ḥarām, even though these floors are higher than the roof of the Ka‘bah itself. And Allah, the Exalted, knows best.
