The children were found by the superintendant just after 10am in the apartment on Bergen Avenue.
The super said she went and knocked on the door of the home after being hit in the head with a piece of paper. When the oldest child opened the door, the super found that they were home alone.
When she asked where their parents were, she was told they were at work.
Police say the parents showed up to the home 45 minutes after the incident and told witnesses she ran out to go to the store, but was only gone for a few minutes. The investigation continues into how long the children were actually alone.
The mother, 37-year-old Cinthia Medina is charged with child abuse and endangering the welfare of two children.
The children were checked out as a precaution at Jersey City Medical Center and have since been released.