The schools targeted for closure are in Queens, Brooklyn, the Bronx and Manhattan.
The vote by the Panel for Educational Policy came early Tuesday morning after a long and contentious meeting.
"We are constantly working with schools to improve their outcomes," Schools Chancellor Dennis Walcott said. "There are, unfortunately, some schools that just do not get better."
Officials say 142 schools have been shut down or approved for phase-out since 2002 when Mayor Michael Bloomberg came to office.
Angry parents and students challenged the decision at a meeting in Fort Greene. However, their demands to keep the schools open aren't likely to make a difference.
Two schools - M.S. 45/STARS Prep Academy in Manhattan and Freedom Academy High School in Brooklyn - will be closed by the end of this school year. The remaining 20 will be phased out over time.
List of Schools: