Scott Stern, 45, was taken into custody by police in Florida after resigning two weeks ago.
WFLA-TV has said the coach considered it a form of discipline.
The second victim, a 17-year-old, alleges Stern told him to strip before using a ruler to spank him.
There are fears other teens may also have fallen victim to Stern.
Parents at the school have reacted with shock and anger at the students’ accusations.
“I think it’s totally inappropriate,” said Lisa Watt. “I don’t think any coach should ever ever go to those boundaries involving children.”