With a staff of attorneys, public intellectuals, ministers and mobilizers, the Washington D.C.–based non-profit has a long history of advocating in the U.S. Supreme Court and working with Congress on issues relating to religious freedom and church-state separation.

The BJC analyzes new legal cases and legislation within the larger framework of how best to protect the First Amendment right to religious freedom for all.

In recent years, the BJC has gone to the Supreme Court and filed amicus curiae (friend-of-the-court) briefs defending a potential employee's right to wear her hijab to work, opposing the travel ban, and opposing certain government-sponsored displays of religion, such as the giant free-standing cross in a government-owned intersection in Bladensburg, Maryland.

Joseph Martin Dawson was elected the organization's first full-time Executive Director, a position he held until his retirement at age 75 on October 13, 1953.

Recent examples include: The BJC supports the Johnson Amendment, the provision in the US tax code that prohibits houses of worship and 501(c)(3) non-profits from partisan campaigning.

In response to Trump's vow to "destroy" the Johnson Amendment and the administration's repeated attempts to repeal the law, the BJC helped bring together thousands of faith leaders and more than 100 denominations to sign letters to Congress asking to keep it.

Federal money, the BJC argues, should not go to rebuilding churches after a disaster, for example, or to a program that only serves Protestants: government-funded services must be available to all, regardless of religion.

The BJC filed a brief on behalf of the state of Colorado, explaining that laws like this one – covering discrimination against "disability, race, [religion], colour, sex, sexual orientation, marital status, national origin, or ancestry" – protect religious liberty.

[16] In 2015, the BJC and 14 other religious groups joined to defend the right of a Muslim woman to wear her hijab at work in Equal Employment Opportunity Commission v. Abercrombie & Fitch Stores, Inc.

[18] To promote its positions, the BJC publishes a wide array of materials relating to church-state separation, including significant coalition statements.

One of the most effective educating tools[citation needed] in recent years was "Religion in the Public Schools: A Joint Statement of Current Law."

The document served as a resource for parents, students, teachers, and administrators throughout the United States and was later condensed and mailed to schools across the country by President Bill Clinton because of its accuracy and reliability.

The Baptist Joint Committee celebrated its 75th anniversary in 2011 and released a special edition of Report from the Capital highlighting the history of the organization.