It was founded in 1997 by Faisal Alam, a Pakistani American LGBTQ+ rights activist, and was registered as a nonprofit organization in the United States until 2011.
The organization grew out of an internet listserve for questioning Muslims from 25 countries, and by October 1998 had developed numerous in-person chapters.
In 2001, Al-Muhajiroun, an international organization seeking the establishment of a global Islamic caliphate, issued a fatwa declaring that all members of Al-Fatiha were murtadd, or apostates, and condemning them to death.
Because of the threat and coming from conservative societies, many members of the foundation's site still prefer to be anonymous so as to protect their identity while continuing a tradition of secrecy.
[6] While Al-Fatiha worked to combat homophobia within Muslim communities, it also felt it faced the challenge of seeking to avoid provoking an Islamophobic reaction among non-Muslims.