The DOE says girls as young as 14 will be able to get the Plan B emergency contraception without parental consent.
Parents have been notified about the CATCH pilot program and how their daughters can opt out of it.
City Council Speaker Christine Quinn says she supports the program because high school students are sexually active and getting pregnant.
The city says about 7,000 girls get pregnant by the time they reach the age of 17. It says more than half choose to get an abortion.
NYC schools already distribute free condoms to students.