A spokesperson for the interior ministry, Tariq Arian, put the death toll at least 25 but did not specify the cause or the target.
Ghulam Dastagir Nazari, spokesperson for the health ministry, said 46 people had been taken to hospitals so far.
Kabul is on high alert since Washington announced plans last month to pull out all US troops by Sept. 11, with Afghan officials saying the Taliban have stepped up attacks across the country.
No group has claimed responsibility for Saturday's attack. Taliban spokesperson Zabihullah Mujahid denied the insurgent group's involvement and condemned the incident.
The explosions took place in western Kabul, a heavily Shi’ite Muslim neighbourhood that has frequently been attacked by Islamic state militants over the years.
The school is a joint high school for girls and boys, who study in three shifts, the second of which is for female students, Najiba Arian, spokesperson for the Ministry of Education, told Reuters.
The wounded are mostly female students, she said.
“The horrendous attack in Dashti Barchi area in Kabul, is a despicable act of terrorism,” the European Union's mission in Afghanistan said on Twitter.
“Targeting primarily students in a girls’ school, makes this an attack on the future of Afghanistan.”