[9] Bernard S. Meyer wrote the trial court opinion ruling that the Establishment Clause "does not prohibit the non-compulsory saying of the Regents' prayer in the public schools".

Meyer's reasoning was based on the "accepted practice" at the time the amendments were adopted:[10][11] The reason the 'establishment' clause is not breached is ... because traditionally, and particularly at the time of the adoption of the First and Fourteenth Amendments, this was the accepted practice.Aside from the historical analysis, the trial court relied on the Supreme Court precedent in Zorach v. Clauson:[10] The Zorach case holds that the Constitution does not require separation in every and all respects and, as we have seen, constitutional history confirms a tradition of prayer, including prayer in the schools...the instant prayer, at least when its recitation is limited to daily exercises at the opening of school, must be classified as outside McCollum's proscription of religious instruction and within Zorach's sanction as an accommodation.The Appellate Division for the Second Department affirmed the trial court's judgment in a per curiam opinion.

[12] Citing Church of the Holy Trinity v. United States, supported by additional reasoning in Zorach v. Clauson, Beldock argued that the Regents' Prayer merely reaffirmed "that this is a religious nation".

[14] In a 6–1 decision (Justices Felix Frankfurter and Byron White did not participate), the Supreme Court held that reciting government-written prayers in public schools was unconstitutional, violating the Establishment Clause of the First Amendment.

[9] Writing for the majority, Justice Hugo Black wrote that recitation of a government-written prayer by school children was "a practice wholly inconsistent with the Establishment Clause" that breached the "wall of separation between Church and State".

"[16][17] Justice Black's reasoning included historical analysis:[18][19] It is a matter of history that this practice of establishing governmentally composed prayers for religious services was one of the reasons which caused many of our early colonists to leave England and seek religious freedom in America.Justice Black's argument that religion is "too personal, too sacred, too holy to permit its 'unhallowed perversion' by a civil magistrate" includes a direct quote from James Madison's Memorial and Remonstrance.

In his dissenting opinion, Justice Stewart contended that the Establishment Clause was originally written to abolish the idea of a state-sponsored church,[2] and not to stop a non-mandatory "brief non-denominational prayer".

Frank J. Becker called it "the most tragic decision in the history of the United States" and introduced a proposed constitutional amendment to allow religious exercises in public schools.

After the Engel decision, some members of Congress, like George Andrews of Alabama and James Eastland of Mississippi, made references to both desegregation and prayer in schools in their attacks on the Warren Court.

Bishop James Pike, a prominent religious moderate and lawyer, opposed the Court's broad interpretation of the Establishment Clause because it prohibited non-denominational prayer.