In an official statement, local Islamic State affiliate ISIS-K identified the bomber as a Uygher Muslim, saying the attack at the Gozar-e-Sayed Abad Mosque in Kunduz targeted both Shiites and the Taliban for their purported willingness to expel Uyghers to meet demands from China.
The death toll stands as the highest since U.S. and NATO forces left Afghanistan at the end of August and the Taliban took control of the country.
The United Nations mission in Afghanistan condemned the attack as "part of a disturbing pattern of violence" targeting religious institutions. The group that gathered at the mosque has been identified as Hazaras, an ethnic minority of Shiite worshippers who make up 6% of the province's population.
A prominent Shiite cleric, Sayed Hussain Alimi Balkhi, called on the Taliban to provide security for the Shiites of Afghanistan.
"We expect the security forces of the government to provide security for the mosques since they collected the weapons that were provided for the security of the worship places," he said.
Mosques are typically crowded during the Friday noon prayer. Witness Ali Reza said he was praying at the time of the explosion and reported seeing many casualties.
"I assure our Shiite brothers that the Taliban are prepared to ensure their safety," said Dost Mohammad Obaida, the deputy police chief for Kunduz province, adding that an investigation was underway.
Taliban leadership have since struggled with the growing threat from local Islamic State affiliate ISIS-K.
The affiliate group claimed responsibility for horrific attack on Aug. 26 that killed 13 U.S. military personnel and 170 Afghan citizens outside the Kabul airport during the U.S. military withdrawal from Afghanistan.
The Associated Press contributed to this report.