A respected Long Island high school choir director has been arrested for sexually abusing a 16-year-old student at his home two years ago, police said Wednesday.

Mark Kimes, 53 — who serves as leader of a National Guard band and won a Bronze Star during his military career — was charged with engaging in a first-degree criminal sex act after the student told detectives he was abused while he attended Hauppauge High School about two years ago, Suffolk County police said.

A judge ordered Kimes, who pleaded not guilty, held on $55,000 cash bail or $105,000 bond at his arraignment Wednesday.

In addition to the alleged sexual abuse, Kimes allegedly gave alcohol to the victim on separate occasions, officials said.

The judge also ordered him to stay away from the victim, a spokeswoman for the Suffolk County District Attorney’s Office told The Post.

Kimes has been reassigned following his arrest and was ordered not to return to school grounds, according to Hauppauge School District Superintendent Dennis O’Hara.

“We will closely monitor this matter and continue to cooperate with the police in their investigation,” the statement read. “Be assured the health and safety of our students is always our first priority.”

In addition to serving as the high school’s chorus instructor, Kimes joined the New York Army National Guard in 1985 and currently serves as commander of the 42nd Infantry Division Band.

He’s also had a decorated military career, earning a Bronze Star, a Meritorious Service Medal and an Iraq Campaign Medal throughout his 34 years in the armed forces, National Guard spokesman Eric Durr told The Post.

A call seeking comment from Kimes’ attorney, James Symancyk, was not returned Thursday.

O’Hara declined to indicate whether Kimes will be paid while on home assignment or whether he has had any prior complaints filed against him, saying it was a “personnel matter” when reached by The Post.

Kimes is scheduled to return to court on Monday.