The ACLJ was founded in 1990 by law school graduate and evangelical minister Pat Robertson with the stated "mandate to protect religious and constitutional freedoms".

In November 2010, the ACLJ asked that the U.S. Justice Department investigate the Congressional Muslim Staffer Association's weekly prayer session on Capitol Hill, alleging that the organization demonstrated "a pattern of inviting Islamic extremists with ties to terrorism to participate in these events".

[16] The ACLJ is a member of the advisory board of Project 2025,[17] a collection of conservative and right-wing policy proposals from the Heritage Foundation to reshape the United States federal government and consolidate executive power should the Republican nominee win the 2024 presidential election.

[19] Sekulow is half-owner of the for-profit corporation Constitutional Litigation and Advocacy Group[19] whose governor and executive officer is Stuart Roth,[22] one of his partners in the law firm and real estate business that declared bankruptcy in 1986.

[25] The ACLJ has been criticized by the ACLU for its stance on putting prayer in public school, and by Americans United for conflating support of separation of church and state with being anti-religious.