Bharti founded the Bharatiya Janashakti party after she was sacked from BJP in 2005.
Bharti told the party's acting president Sanghpriya Gautam that she was quitting the party "in view of the political situation in the country" and her "state of health".
In a letter to Gautum, the 51-year-old leader said that the responsibility of being Bharatiya Janshakti party president along with her desire for "introspection and contemplation with free mind" was proving too stressful for her body and mind.
"Therefore, I am resigning from party presidentship and relieving myself of all responsibilities," the former Madhya Pradesh Chief Minister said.
There have been reports that BJP was ready to take back some sacked leaders as new party chief Nitin Gadkari has expressed interest in allowing re-entry of some popular leaders.