Bronx, NY — A beautiful blond music teacher has been busted for allegedly having a torrid affair with an underage special-ed student.

Emily Streb, 23, was arraigned yesterday on third-degree rape and other charges at Bronx Criminal Court for allegedly having sex with a 16-year-old, whose name is being withheld because of the nature of the charge.

“The complaining witness is a special-ed student who suffers from psychiatric problems,” Assistant DA Heather Cook told Judge Ralph Fabrizio. “She was his music teacher.”

The two had sex “multiple” times at the teacher’s Bronx home from last October to November, and in the evening or early morning at the student’s Bronx home in December, Cook said.

“At 5 o’clock in the morning? In the middle of the night?” Fabrizio asked incredulously.

Stressing that the boy is in special education, the jurist ordered prosecutors to call the city Administration for Children’s Services to protect the boy from his inattentive mother, who apparently wasn’t home at the time.

The prosecutor, who explained that the boy’s mother suffers from depression and other problems, indicated child-welfare officials had already gotten involved.

School authorities learned late last year that there was something off key between teacher and student at PS 12, a special-ed school in The Bronx, and reported it to the schools special investigator, authorities said.

The boy repeatedly denied the claims to school probers in December, according to Streb’s lawyer, Virginia LoPreto.

Still, the teacher was reassigned to the regional office until the lawyer negotiated her resignation independent of the probe. The resignation was effective Feb. 1, officials said.

Ultimately, school authorities contacted the student’s mother, who asked her son about the allegations.

“He finally admitted it to her, and then it was reported to the police [on Monday],” the prosecutor said. That’s when cops arrested Streb at home.

The defense lawyer suggested the boy changed his tune recently because he felt jilted by the teacher. He sent “threatening” text messages to the 5-foot-4, 125-pound instructor on Thursday, according to LoPreto.

And the messages were no serenade.

“I told you you better watch your back,” LoPreto said the boy typed to the teacher.

“We were concerned for her safety,” she said, adding, “He either was told something about her or heard something about her that upset him . . . One could say . . . he indicated that he had been dropped.”

The judge released Streb without setting bail, but he issued a full order of protection, barring her from contacting the student.