Prayer and the Pledge of Allegiance in public schools remain controversial legal issues. Since the mid-twentieth century, the federal courts have placed limits upon state power to require or even permit these popular cultural practices. Two landmark Supreme Court decisions in the 1960s banned prayer in public school, and subsequent decisions have mostly strengthened the ban. By comparison, the courts generally have held since the 1940s that the Pledge of Allegiance is permissible, provided that it is voluntary. Nonetheless, some individuals have brought lawsuits in the 2000s, arguing that the Pledge violates the Establishment Clause of the First Amendment to the U.S. Constitution because the Pledge contains the phrase "under God."

Prayer was a common practice in colonial American schools, which were often merely offshoots of a local Protestant church. Along with Bible study, this tradition continued after U. S. independence and flourished well into the nineteenth century. But historical forces changed education. As immigration multiplied the ethnic and religious identities of Americans, modernization efforts led by education reformers like Horace Mann gradually minimized religious influences in schools. Although this secular reform swept cities, where diverse populations often disagreed on what religious practice to follow in schools, much of the United States retained school prayer.

As the twentieth century brought legal conflicts, the stage was set for even more far-reaching changes. From 1910 onward, lawsuits challenged mandatory Bible reading in public schools on the ground that students should not be forced to practice a faith other than their own. By the mid-century, social and religious tensions had pushed litigation through the federal courts. Subsequently, the Supreme Court ruled repeatedly that school prayer, Bible reading, and related religious practices are violations of the First Amendment. The decisions stand as critical modern mileposts in the contest between federalism and states' rights:

• The Supreme Court first ruled against public school prayer in the 1962 case of Engle v. Vitale. The decision struck down a New York State law that required public schools to begin the school day either with Bible reading or recitation of a specially-written, nondenominational prayer.
• One year later, in District of Abington Township vs. Schempp (1963), the Supreme Court struck down voluntary Bible readings and recitation of the Lord's Prayer in public schools.
• In 1980, in Stone v. Graham, the Supreme Court ruled against a Kentucky law that required the posting of the Ten Commandments in all public school classrooms.
• In 1981, the Supreme Court ruled in Widmar v. Vincent that a state university could not prohibit a religious group from using facilities that were made open for use by organizations of all other kinds. Congress responded three years later with the Equal Access Act, guaranteeing religious student groups the same rights of access to school facilities as other student groups.
• In the 1980s and 1990s, some states enacted so-called "moment of silence" or "minute of silence" laws with the intent of allowing students to conduct private prayer or spiritual reflection in the classroom. Although the Supreme Court found an early Alabama law unconstitutional in Wallace v. Jaffrey (1985), subsequent laws have generally survived legal challenges.
• In 1992, in Lee v. Weisman, the Supreme Court ruled that school officials violated the First Amendment by inviting clergy to give an invocation and a benediction at a public high school graduation.
• In Santa Fe Independent School District v. Doe (2000), the Supreme Court ruled against a Texas school district policy of facilitating prayers over the public address system at football games and holding popular elections to choose the student selected to deliver the prayer.

The Pledge of Allegiance is one of the nation's most honored secular symbols, viewed by many in the same light as the National Anthem. Written in 1892 by the socialist Francis Bellamy, the Pledge of Allegiance first appeared in a national family magazine, Youths' Companion, and later was modified by Congress and President Dwight D. Eisenhower in 1954 to include a reference to God. Many public schools featured the pledge as part of the school day throughout the mid-twentieth century.

Legal controversy in public schools grew out of a dispute over religious freedom. In the 1930s, West Virginia mandated compulsory saluting of the flag and recitation of the Pledge. After members of Jehovah's Witnesses objected on religious grounds, students were expelled from school. The Supreme Court first upheld the state law but reversed itself three years later in West Virginia State Board of Education v. Barnette (1943). The Court held that schools may not coerce or force students into reciting the Pledge, observing the existence of an individual right of conscience to sit silently while others recited. Most schools responded by making the Pledge of Allegiance voluntary.

Contemporary legal challenges to the Pledge have been sporadic, yet they are still passionate and often draw considerable interest from the press. High-profile cases in the late 1990s and 2000s involved lawsuits against schools that instituted mandatory requirements and punished students who did not comply. Interest in the issue intensified again in 2001 following terrorist attacks upon the United States, which prompted states and school districts to revive long-dormant laws requiring students to recite the pledge. The U.S. Supreme Court in 2004 agreed to review a case involving the question of whether the Pledge of Allegiance violates the Constitution, but the Court decided the case on procedural grounds and did not rule on the constitutionality of the Pledge.