It happened around 2:44 a.m. on 401 Centre Street.
Officers say Bradley Price, 36, had been watching his three children, ages two, four and ten while the mother was away at work.
The woman told police she had just come home when she found the two younger children with bruises and other marks on their bodies.
According to police, the ten-year-old had been sent outside, sometime during the late evening, and the child could hear the younger two screaming inside the house.
Price is charged with two counts of child abuse resulting in injury.
Police say the children were taken to Martinsburg City Hospital and have been released to their mother's care.
This case remains under investigation by the Martinsburg Police Department and the Department of Health and Human Resources.