Jamitha, 34, general secretary of the Quran Sunnat Society, had conducted the Jumu'ah, the Muslim Friday prayer service, at the Society's office in Malappuram district's Wandoor village last Friday.
Jumu'ah prayers, held every Friday, are usually led by men.
"Comments and threats have been posted on social media saying I should not be allowed to live... that I should be burnt alive as I am destroying Islam," Jamitha told PTI.
She said she would not be cowed down by the threats and would continue to lead the prayers.
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"Those who are attacking me through social media are cowards," she said, adding that she had not filed a police complaint.
Popularly known as 'Jamitha teacher' in the area, she said the Quran does not discriminate between men and women and Islam doesn't stop women from becoming imams.
About 80 people, including women, had attended the prayers, led by the woman 'Imam', Society sources had said.
The CBI, which probed his disappearance, concluded that he had been murdered and his body disposed of in a mysterious manner.
Jamitha's radical move has kicked up a wide debate on social media.