The 18-year-old student at City-As-School, located at 16 Clarkson St., hit his 30-year-old female teacher with the stun gun once in the back and once in the front of her body a little before 1 p.m., police said.
Police said the student and the teacher had exchanged words before the incident, but it was unclear whether they were arguing.
The teacher was taken to New York-Presbyterian/Lower Manhattan Hospital in an ambulance, police said.
The student fled the school and had not been apprehended as of later Thursday afternoon, sources said.
Brandon Wilkins, a 20-year-old student at the school, didn't witness the incident, but said the school was put on lockdown for about an hour afterward.
The school, which offers an alternative path to high school graduation to students who have struggled to gain credits at traditional programs, did not immediately respond to a message left for comment.
The Department of Education did not immediately respond to requests for comment.