Is it permissible to perform Iʿtikāf in mosques other than the three mosques? (al-Masjid al-Ḥarām, al-Masjid al-Nabawī and al-Masjid al-Aqsā) and what is the evidence?
Yes, it is permissible to perform Iʿtikāf in mosques other than the three mosques- al-Masjid al-Ḥarām, The Prophet’s mosque (peace be upon him) and al-Masjid al-Aqsā. The evidence for this is the generality of Allah’s saying (And do not have sexual relations with them (your wives) while you are in Iʿtikāf (i.e. confining oneself in a mosque for prayers and invocations leaving the worldly activities) in the mosques.)
This verse addresses all Muslims and if we were to say that the intended meaning was restricted to the three mosques then most Muslims would be excluded as most Muslims are outside Makkah, Madīnah and Jerusalem.
Based on this we say performing Iʿtikāf is permissible in all mosques. And if the hadīth which says (there is no Iʿtikāf except in the three mosques) is authentic, the intended meaning would be the negation of the most complete or best Iʿtikāf. And there is no doubt that performing Iʿtikāf in the three mosques is better than performing it elsewhere just as performing ṣalāh in the three is better than elsewhere.
Majmūʿ Durūs Wa Fatāwā Al-Ḥaram Al-Makkī, Muḥammad b. Ṣaliḥ Al- ʿUthaymīn, Volume 3, Page 49