A Queens substitute teacher was busted for allegedly threatening to shoot a class of middle schoolers if they didn’t listen to him Wednesday, according to police sources. 

Alejandro Rocha, 52, was teaching a group of nine kids, ages 11 and 12, at IS 5-The Walter Crowley Intermediate School in Elmhurst, just after 2 p.m. Wednesday when he made the disturbing remark, the sources said. 

“If you don’t do what you’re told, I’m going to shoot you — and yes, I have a gun,” Rocha allegedly snarled. 

Rocha later ‘fessed up to a supervisor and apologized, claiming it was all a bad joke, according to the sources.

He was arrested more than four hours later and charged with making a terroristic threat, police said. 

“This is absolutely unacceptable,” a Department of Education spokesperson said in a statement. “The substitute teacher was immediately suspended and if this deeply disturbing allegation is found to be true, he will be fired.”

Rocha began as a substitute teacher in September 2001 and has no prior disciplinary history, the department said. He has been suspended without pay and not currently eligible to work in city schools.