Heather Barron, arrested Friday, was also charged with torture in the death of Anthony Avalos. She did not enter a plea while in front of a Lancaster judge and her arraignment was postponed.
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Barron's boyfriend Kareem Leiva, 32, was arrested Wednesday on suspicion of murdering Avalos.
Avalos died June 21, a day after he was found unresponsive, and authorities deemed his death suspicious.
Barron claimed that the boy fell and injured his head, while detectives believe that she and Leiva tortured him to death.
Leiva was taken into custody earlier this week, although he has yet to appear in court due to hospitalization for a previous injury - a cut to his chest that detectives believe was self-inflicted.
The L.A. County Department of Children and Family Services has since removed eight children from the home and taken custody of them.
Since 2013, DCFS reported receiving at least a dozen referrals for possible physical, emotional and sexual abuse of the boy. No such reports had been made in the last two years. Authorities are reviewing the agency's response to those reports.
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Authorities said Avalos' sexuality may have been a motivating factor in his death.
DCFS Director Bobby Cagle told Eyewitness News that the department is investigating whether homophobia played a role in the boy's death.
"One of the things that we have heard is that there may have been a motivation on the part of the man in the household regarding to the sexuality of the child, and so we're looking into that in a very deep way," Cagle said.
Family members of Avalos and their attorney gathered in front of the organization's office in Lancaster on Friday afternoon to demand transparency.
If convicted of the charges against her, Barron faces a possible maximum sentence of 22 years to life in state prison. Leiva faces 32 years to life if convicted.