The boy, identified as Gaurav Kank, plunged to his death from the window of the classroom at New Horizon Public School in New Panvel area yesterday at around 10.30 AM.
The minor, who was found in a pool of blood on the ground, was rushed to a nearby private hospital where he was declared dead.
"The science teacher, Saumya Manoharan, was arrested last night under IPC sections 306 (abetment of suicide) and 304 A (causing death by negligence)," Deputy Police Commissioner Sanjay Singh Yenpure said.
"Following the episode, the class VIth student went back to his classroom. After a while, the recess was announced. Gaurav then jumped from a partially grilled window of the classroom," Yenpure said.
Several students of his class reportedly saw him plunging.
Gaurav used to stay at Khanda colony with his parents, who run a small electrical appliances store in the area.