Andrea D. Jackson, 23, turned herself Thursday, authorities said.
Earlier in the day, prosecutors filed charges of dealing and possession of cocaine, neglect of a dependent and possession of marijuana against Jackson and the boy's father, Kenneth Green, 24.
Marion County Prosecutor Carl Brizzi said Green was the main dealer in this case.
Prosecutors filed the charges three days after the boy brought a bag of crack cocaine in his book bag to a Head Start program.
Police who later searched the couple's home said they found a handgun and rifle rounds, shotgun shells and a bulletproof vest, scales and some suspected marijuana.
Some of the drug dealing and drug use was done in front of the children, Brizzi said.
Green's mother, Rhonda Ingram, 45, told the Indianapolis Star she doubted her son was dealing drugs.
"If he did drugs, I would know it," she said. "He is too good of a father to do that. He is a role model to those kids."
The children, an infant and siblings ages 4, 6 and 7, are now in protective custody.