The ICC said there were reasonable grounds to believe that Akhundzada and Abdul Hakim Haqqani, chief justice of the Taliban, had committed the crime against humanity of persecution on gender grounds against girls, women and other persons non-conforming with the Taliban's policy on gender, gender identity or expression.
Since the Islamist Taliban returned to power in 2021 it has clamped down on women's rights, including limits to schooling, work and general independence in daily life.
The Taliban condemned the warrants as an example of hostility towards Islam.
"We neither recognise anything by the name of an international court nor do we consider ourselves bound by it," the Taliban government's spokesman, Zabihullah Mujahid, added in a statement.
It is the first time judges of the ICC have issued a warrant on charges of gender persecution.
"While the Taliban have imposed certain rules and prohibitions on the population as a whole, they have specifically targeted girls and women by reason of their gender, depriving them of fundamental rights and freedoms," the court said.
The full warrants and details on the specific incidents they are based on remain under seal to protect witnesses and victims, the court said.
NGOs hailed the warrants and called on the international community to back the ICC's work.
"The international community should fully back the ICC in its critical work in Afghanistan and globally, including through concerted efforts to enforce the court's warrants," Human Rights Watch International Justice director Liz Evenson, said in a statement.
The ICC has been under increased criticism from non-member states such as the United States, Israel and Russia.
Last year the court issued an arrest warrant for Israeli Prime Minister Benjamin Netanyahu for alleged war crimes and crimes against humanity during the Gaza conflict. The ICC also issued an arrest warrant for Russian President Vladimir Putin in 2023 on suspicion of deporting children from Ukraine.
Neither Russia nor Israel is a member of the court and both deny the accusations and reject ICC jurisdiction.
Last month the United States imposed sanctions on four ICC judges including two who were involved in a ruling that allowed prosecutors to open a formal investigation into war crimes and crimes against humanity in Afghanistan, including alleged crimes committed by American troops.
The ICC said it was an attempt to undermine the independence of an international judicial institution that provides hope and justice to millions of victims.
