The 18-year-old fell at the New Charter Academy on Broadoak Road in Ashton-under-Lyne at about 09:10 BST, Greater Manchester Police (GMP) said.
GMP said he had gone to Manchester Royal Infirmary and his condition was "serious".
Principal Jenny Langley said the school would remain "fully open" while police investigated.
"Our thoughts are with the family and we're doing everything we can to support them along with staff and pupils," she said.
A student has been taken to hospital after falling from a balcony at a Greater Manchester school.