In a 6–3 decision the Court ruled that Maine's restrictions on vouchers violated the Free Exercise Clause, as they discriminated against religious schools and the parents who chose them for their children.

[2] Since 1873, Maine has provided tuition assistance for residents of those areas to send their children to nearby public or private schools of their choice.

In the first, Trinity Lutheran Church of Columbia, Inc. v. Comer, the Court ruled that denying a Missouri religious school the funds to resurface a playground while providing such funds to non-religious schools violated the Free Exercise Clause of the First Amendment, and that government programs cannot discriminate on the basis of religious status.

[1][7] The filing argued that per Trinity Lutheran, "The government must remain neutral with regard to religion—neither favoring nor disfavoring it—and the participants must exercise a genuine choice between religious and nonreligious options.

[9] The First Circuit upheld the district court's ruling, ruling that since Maine's program based its voucher allowance on whether schools teach and proselytize religion with the voucher funds, rather than whether schools are run by religious organizations, the program fell within the separation of church and state.

[10] The Cato Institute, Hillsdale College, The Church of Jesus Christ of Latter-day Saints, and the Americans for Prosperity Foundation filed amicus briefs in support of the petitioner, and The Freedom From Religion Foundation, The American Civil Liberties Union, and the National School Boards Association filed amicus briefs in support of the respondent.

[12] In his majority opinion, Roberts wrote that the State violated the First Amendment's Free Exercise Clause by preventing religious observers from receiving public benefits.

The Court ruled that Maine purposely "identif[ies] and exclude[s] otherwise eligible schools on the basis of their religious exercise" and that that is "discrimination against religion".

[15] Breyer expressed concern that Carson v. Makin could require states to fund religious schools with taxpayer money, writing that the ruling paid "almost no attention" to the First Amendment's prohibitions on the state's establishment of religion while "giving almost exclusive attention" the Amendment's prohibitions on religious free exercise.

[16] He also wrote that the ruling broke with historical precedent, that Supreme Court had "never previously held what the Court holds today, namely, that a State must (not may) use state funds to pay for religious education as part of a tuition program designed to ensure the provision of free statewide public school education.