The petition asks that two teenage children she has with her husband be removed from Lyle Jeffs' compound in Hildale and placed with her or into protective custody.
The documents in the petition show that Judge Paul Dame did not find the children were in imminent danger and declined a request to remove the youths immediately. A hearing has been scheduled to hear oral arguments.
Attorneys for Charlene and Lyle Jeffs did not respond to requests for comment Friday.
The petition was filed with the court April 10. It was fastened to the compound door in an effort to serve Lyle Jeffs and has been circulated among people who have left the FLDS.
Lyle and Charlene Jeffs have been married since August 1983 and have 10 children together, the petition says. The two teenagers discussed in court documents, a 17-year-old boy and a 14-year-old girl, appear to be the youngest.
Charlene Jeffs says she has been "excluded" from the teens' lives for about three years.
"Of Lyle's multiple wives, I was never the favorite because I have a mind of my own," Charlene Jeffs wrote in the petition. "Lyle sent me away from the family to repent for the first time in November 2002 because 'I did not know how to properly treat the Priesthood in my life.' "
FLDS leaders are referred to as "the Priesthood."
Charlene Jeffs goes on to write that in the first year of her exile, she was allowed to live in the family home but not to mother her children.
"I could cook and clean but do no more," she wrote. "In the FLDS Church, children belong to the Priesthood and can be transferred to different mothers or different parents all together upon an order from the Priesthood."
In the second year of her exile, Charlene Jeffs said, she was moved to a guest house in Hildale. She returned to the family home after two years of repenting, but has not been allowed to rear her children since then, she wrote. Care for the children has been rotated among her husband's so-called spiritual wives, she wrote.
Other members of Lyle Jeffs' family who have left the FLDS have said Charlene Jeffs was the first of nine wives. One of the spiritual wives is Pauline Barlow, and she is named as a respondent in the custody petition.
Charlene Jeffs said she was ordered to leave her husband's compound Sept. 27, 2014, for being "unrighteous." She has not been allowed to see the teens since then.
Charlene Jeffs asked the judge to remove the children immediately before her husband realized she had no interest in returning to the FLDS.
"The Jeffs family is the FLDS equivalent of the British Royal Family and they have their own FLDS 'secret service' to protect them from the outside world," Charlene Jeffs explained in her petition. "If Lyle had any idea that I have gone 'apostate,' he would make my children disappear to one of the many hidden FLDS communities in the U.S., Canada, Mexico or somewhere new altogether, and I would never find them."