Nassau County police took John Omard, the principal at J.W. Dodd Middle School in Freeport, into custody.
The 44-year-old O'Mard was awaiting arraignment Wednesday on four counts of third-degree criminal sex act.
It's alleged that he arranged to meet the 16-year-old in September of 2012, drove the boy to his Freeport home and engaged in sex acts with the victim. The victim was not legally able to consent due to his age.
The boy's age leads police to believe he was likely not a student at the school.