Margaret Gieszinger, 52, has also lost her job at University Preparatory High School in Visalia, California.
Prosecutors say she has pleaded not guilty to the six charges, including child cruelty and battery, and faces up to three-and-a-half years in prison.
Ms Gieszinger was released on a $100,000 (£78,500) bail late on Friday.
In mobile phone video posted to Reddit, the science teacher is seen calling a male student to sit at the front of the class. She then cuts chunks of his hair while singing an incorrect version of the Star Spangled Banner.
A lawyer for the student told CNN his client was "absolutely terrified" before he managed to get away.
Ms Gieszinger is then seen holding the scissors above her head, saying "Next!" before threatening to cut a female student's hair.
"We take very seriously the safety of the students in classrooms," the Tulare County Office of Education said in a statement.
"We are reviewing all available information and will take the most severe employment action appropriate."