Students and parents were given notice about the testing 90 days ago.
Some are not happy with the new rules and others ask if drug testing even makes a difference.
"The drug testing, I don't mind it because I personally don't use any of that, but I do think it is an invasion of our privacy," senior Brendan Donnelly said.
"I would say most students are not with it; I would say a small minority would be for the testing," senior Tom Coar said.
Principal Jason Zazyczny and Director of Counseling Bill Gillespie say they did not make this decision lightly and they say it is not to punish but to protect the students.
"This is their formative years, their high school years, teenage years and the more we can help them to make better decisions we're going to do that and we feel by instituting a policy like this, this will help them in their future," Zazyczny said.
"While people may not agree with our stance, I, at least, would hope they know we have the best interest of the students in mind." Gillespie said.
Starting next month, 10 students will be chosen by lottery twice a month and their hair will tested.
Urine tests show drug use in the past days to weeks, but hair tests can show if someone has used drugs over the past several months.
Sandra DiWilliams, a licensed professional counselor who specializes in adolescent addiction, says some studies show random drug testing prevents drug use, while others show it doesn't make a difference.
But she says it does give some teens an easy excuse to say "no," despite mounting peer pressure.
"Some kids can use their sports teams as an excuse or they have a pending scholarship. Some kids don't have excuses that they think are good so drug testing can be a good one," DiWilliams said.
If a student fails the test, he will not be punished, but will have to go to counseling and submit more tests, paid for by his parents.
If a student fails twice, he could get expelled, but the principal says it will be a case by case decision.
Also of note, St. Joseph's Prep, being a private school, can legally drug test the entire student body, whereas public schools can only do limited testing, such as for students in extracurricular activities.
Malvern Prep in Chester County, meanwhile, has already been performing universal drug testing using the same company as St. Joseph's.