The incident was reported on July 25th at a facility at the Sprouts day care in the 600 block of South 9th Street.
The victims are one boy and one girl, both five years old.
The owner, 53-year-old Duncan Round of Medford Lakes, New Jersey, has been arrested. He is charged with rape, sexual assault and related offenses.
Police are working to figure out if there are any other victims.
They are asking any parents with concerns to contact police.