Farideh Moradkhani, in an eight-minute video of posted by her brother Mahmoud, speaks out against the “child-killing regime”.
“Tell your government to stop supporting this murderous and child-killing regime,” she says.
Ms Moradkhani is the daughter of Mr Khamenei's sister Badri, with whom he has strained relations. Her father, Ali Tehrani, was sentenced to 20 years in prison in 1995.
Her Twitter page shows that she is based in Tehran, and has posted anti-government tweets dating back years.
Ms Moradkhani's brother Mahmoud, who is a doctor in France, said she was arrested earlier this month. It is unclear whether she had been arrested before the video was posted.
In the video, Ms Moradkhani also criticises the role played by the UN in responding to the protests that broke out in September 16.
They followed the death of Kurdish-Iranian woman Mahsa Amini, 22, while in the custody of the morality police in Tehran. She had been detained for wearing her hijab “improperly”.
“What has the UN done in front of this clear and obvious cruel oppression that is perpetrated on brave Iranians, other than a few expressions of regret and short and ineffective statements?” Ms Moradkhani asks.
Last week, the US issued sanctions against government officials it accused of complicity in the “extrajudicial killing” of protesters.
Ms Moradkhani calls western sanctions on Iran “ridiculous and laughable” and praised the role of women in the demonstrations.
“For the first time in human history, women are dictating their hidden power over this patriarchal society and showing with all the courage that the place of real power is in the thought and not in the muscle,” she says in the video.
Demonstrations have spread across the country and evolved into calls for the regime's removal.
Last week, the UN's Office of the High Commissioner for Human Rights said more than 300 people had been killed in the protests.
Mohammad Al Zghool, Iranian affairs researcher at Abu Dhabi-based think tank the Emirates Policy Centre, told The National these protests have bridged the “fault lines” across Iran's economic, ethnic and class divides.
“The protests built bridges between the lower and middle class, making the protests multinational and multi-ethnic,” he said.
In previous protests, this has not always been the case, Mr Al Zghool said.
“The middle class usually does not respond to lower-class protests, and vice versa,” he added.
Similarly, where one ethnic group protests, others usually do not join in, said Mr Al Zghool.
However, in recent weeks, protesters from the Baloch ethnic group clashed violently with security forces where hundreds were killed.
“This is despite the fact that the Baluchis [Balochs] are relatively conservative and are not usually concerned with hijab-related issues, Mr Al Zghool said.
“Similarly, in Kurdistan [province], we witnessed the second-most violent clashes there.”
Mr Al Zghool said it was clear that the regime was concerned about the protests.
Iran has accused foreign powers of fomenting unrest, without providing any evidence. It has also launched attacks on Iranian Kurds exiled in Iraq.