Answer:
Prayer in schools is not a violation of the first amendment so long as it is voluntary and not coerced.
However, the Supreme Court has ruled that public schools cannot lead students in prayer or organize other activities that endorse religion. According to the court, doing so would constitute a violation of the Establishment Clause of the First Amendment which states that "Congress shall make no law respecting an establishment of religion". Numerous cases have been argued before the court about what constitutes coercion as well as whether a specific religious activity is truly voluntary.
In 2000, for example, the court ruled in Santa Fe Independent School District v. Jane Doe that public schools cannot provide a forum for student led-prayer to be broadcast over the public address system prior to an athletic event even when the choice to engage in the prayer and who would lead it was made by the students. The court has stated over the years that the establishment clause must prohibit schools from engaging in behavior that promotes religion (or one religion over another) because students of high school age and younger are impressionable and have not yet necessarily formed their own independent belief systems.