Catherine Allex, 34, was arrested late Wednesday night after a search that lasted more than 24 hours.
Police say Allex's 11-year-old son and a 10-year-old boy, also in her care, were home alone when one of them ran to a neighbor's house.
"A neighbor reported a hysterical child came to their house, thinking someone was in the home. Our officers responded and found there was nobody in the home," said Lt. Mark Farrall of the Newark Police Department.
However, what police did find inside the four bedroom, two-and-a-half bathroom home on Tuesday night led to the code enforcement officer to seal the home, calling it 'uninhabitable.'
"Our officers observed there was disarray, garbage strewn throughout the house, animal feces and no sign of food for the children at that time," said Lt. Farrall.
At the time, investigators couldn't find Allex or a 9-year-old girl and a 2-year-old boy believed to be with her.
Authorities took the boys as police searched for Allex and the other children, who were finally found late Wednesday.
Speaking to Action News, Allex challenged the police timeline.
"I returned home and saw that my son was gone so I went and I took my other two children to a safe place and then returned," Allex said.
For now the four children are with the division of family services.
Allex is charged with two counts of child endangerment, and the house she rents remains sealed.