Students may pray non-disruptively in any free time they have. No one is trying to take those rights away, no matter what the fundamentalists keep trying to claim. Students HAVE been stopped when they disrupt other students or classtime, or preach to other students, as this infringes on the rights of others.
Faculty, staff, and administration of public schools may not have any open demonstration of religion, however, as they are representatives of the government and thus by the Constitution cannot endorse any religion.
I personally go to a school that is a church! We always have to go to church every morning before we do schoolwork! And it is specifically called Morning Prayer! Even though it is called Morning Prayer though, we still pray a lot of prayers. On Wednesday, though, we have Eucharist. My school even baptizes! On Wednesday, October 23, 2013, A classmate of mine was baptized. I go to St. Mark's Episcopal School.
The current law (which I agree with) basically says that if you want to pray, it's on your time, and it can't be disruptive or harmful. I just posted this question, because it is a large myth that prayer is not allowed in schools, and that atheists are trying to "get rid of religion", but that's not true. The law is that mandatory prayer is not allowed, but if someone wants to they can.
Prayer is currently permitted on US school property- however, mandatory school prayers are unconstitutional and are therefore banned. Other than that I can't say much else, but I have to continue speaking to meet the 50 word quota so that I can point this out. Also, this topic should be locked.
Oftentimes, separation of church and state is taken farther. Students are told they cannot mention their god or their religion. Students are told they cannot pray. Students are even suspended for praying in school! While schools shouldn't make someone pray or encourage religion, they should allow each student to practice their religions in non-intrusive ways.