Thomas Barnhart, 54, was charged after turning himself in on Wednesday.
Barnhart works as a Special Education Coordinator for the Red Clay Consolidated School District and is still listed on the website.
The incidents happened during sleepovers at his home on Skylark Road and were reported in April of this year.
The inappropriate contact with the girls happened between November 2021 and July 2023, police said.
According to the criminal complaint, the two 9-year-old girls woke up to him assaulting them on separate occasions.
One victim says she had numerous other encounters where she would wake to 'Mr. Tom' standing over her.
When police interviewed Barnhart, he claimed he would adjust the kids' bedding as they slept but that he would, quote, "probably fail a polygraph examination if he took one, due to his nerves."
Police say the Red Clay Consolidated School District was notified and is cooperating with the investigation.
Investigators say there is no evidence at this time suggesting that any students from the school district were involved as victims.
Barnhart is being held on more than $100,000 cash bail.
Police say they are concerned there are more victims who have not yet come forward.
Anyone with information is asked to contact Detective Matthew Donovan at (302) 395-2781 or via email at Matthew.Donovan@newcastlede.gov.