The United States Supreme Court ruled in Employment Division v. Smith (1990) that a person may not defy "neutral laws of general applicability"[a] even as an expression of religious belief.

In 1993, the U.S. Congress responded by passing the Religious Freedom Restoration Act (RFRA), requiring strict scrutiny when a neutral law of general applicability "substantially burden[s] a person's[b] exercise of religion".

[6] The Little Sisters of the Poor, a Catholic religious order, runs over 25 homes for low-income elderly in the United States[7] and therefore is not automatically exempt from the contraceptive mandate.

On December 31, 2013, the day before the filing requirement was to come into effect, Supreme Court Justice Sonia Sotomayor granted a temporary injunction to the Little Sisters of the Poor, allowing them to simply inform the Secretary of Health and Human Services of their objections, pending resolution of the case.

[14] On July 3, 2014, the Supreme Court granted a temporary exemption to the approach it suggested as a less restrictive alternative in Hobby Lobby, where the plaintiffs would send an EBSA Form 700 to its insurance issuer, which would pay for the contraception.

The court said "Nothing in this interim order affects the ability of the applicant's employees and students to obtain, without cost, the full range of FDA approved contraceptives.

"[15] In a 15-page dissent, joined by the other two female jurists on the court, Justice Sotomayor criticized the majority's reasoning and distinguished it from the situation with the Little Sisters of the Poor.

[16] A revised version of EBSA Form 700, effective August 2014, says "[a]s an alternative to using this form, an eligible organization may provide notice to the Secretary of Health and Human Services that the eligible organization has a religious objection to providing coverage for all or a subset of contraceptive services..." Eight appeals courts upheld the ACA mandate for non-church religious institutions.

Only the Eighth Circuit Court of Appeals ruled the other way, upholding the challenge by religious non-profit institutions in September 2015 in two cases, Sharpe Holdings v. HHS and Dordt College v.

[31] Because the Petitioners agreed that "their religious exercise is not infringed where they 'need to do nothing more than contract for a plan that does not include coverage for some or all forms of contraception'", the Court held that the parties should be given an opportunity to clarify and refine how this approach would work in practice and to "resolve any outstanding issues".

This led to numerous states pursuing further legal action on the new rules that culminated in another Supreme Court case, Little Sisters of the Poor Saints Peter and Paul Home v. Pennsylvania, which was heard in May 2020.