Helen Sarkar, the principal of the school at Dum Dum, was arrested for negligence of duty, a day after death of the 11-year-old student, kept confined inside a toilet allegedly by her seniors, police said.
Earlier in the day, succumbing to mounting pressure, the principal had tendered her resignation.
She will be produced before the Additional Chief Judicial Magistrate in Barrackpore tomorrow.
Chief Minister Mamata Banerjee talked to the student's mother Rekha Das and consoled her, assuring that she would look into the incident.
The agitators, who laid a siege to the main gate of the school, demanded that the principal be immediately arrested and a probe conducted into the incident.
"We demand immediate arrest of the principal and punishment of those responsible for Oindrila's death," they said.
A combat police force was posted outside the school as the guardians ransacked the institution since morning.
Meanwhile, police said another case has also been registered against those who ransacked the school.
The principal, who along with six other teachers, was confined within the school because of the agitation, earlier apologised to the angry guardians and said an inquiry would be held into the student's death.
"The incident is unfortunate and we will take all steps to ensure that such incidents do not recur," the principal said over a microphone from the first floor of the school, urging the guardians to be patient.
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