Afghan universities will be segregated by gender, and a new Islamic dress code will be introduced, the Taliban said on Sunday.
Higher Education Minister Abdul Baqi Haqqani indicated women would be allowed to study, but not alongside men.
He also announced a review of subjects taught.
Women and girls were banned from schools and universities under Taliban rule between 1996 and 2001.
The announcement of the higher education policy comes a day after the Taliban raised their flag over the presidential palace, signalling the beginning of their administration. They seized control from the elected government a month ago.
The policy marks a significant change from the accepted practice before the Taliban takeover. Universities were co-educational, with men and women studying side by side, and female students did not have to abide by a dress code.
But Mr Haqqani was unapologetic about bringing an end to mixed classes. "We have no problems in ending the mixed-education system," he said. "The people are Muslims and they will accept it."
Some have suggested that the new rules will exclude women from education because the universities do not have the resources to provide separate classes. However, Mr Haqqani insisted there are enough female teachers and that where they are not available alternatives will be found.
"It all depends on the university's capacity," he said. "We can also use male teachers to teach from behind a curtain, or use technology."
Girls and boys will also be segregated at primary and secondary schools, which was already common throughout Afghanistan.
Women will be required to wear hijabs, however Mr Haqqani did not specify if additional face coverings would be made compulsory.
Uncertain times ahead for Afghan women
The newly installed minister also said that the subjects taught in universities will be reviewed. He told reporters that the Taliban wanted to "create a reasonable and Islamic curriculum that is in line with our Islamic, national and historical values and, on the other hand, be able to compete with other countries".
The announcement comes after a demonstration by women supportive of the Taliban's gender policies at Shaheed Rabbani Education University in Kabul yesterday.
Hundreds of women, most of them wearing black niqabs and carrying small Taliban flags, listened to speeches that praised the new regime and attacked those involved in large demonstrations across the country demanding the protection of women's rights.
The Taliban have attempted to project a more moderate image to the watching world since their dramatic advance saw them overrun government forces in days. They have pledged to respect progress made in women's rights and promised that women will have a place in civil society.
However, there have been signs that the group may govern in the same restrictive way they did during their last stint in power.
A women's march in Kabul was broken up last week when Taliban officials targeted demonstrators with tear gas and pepper spray and the deputy head of the Taliban's cultural commission has said that he doesn't think the women's national cricket team will be allowed to continue.