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The dean of students at Timilty Middle School in Roxbury is facing aggravated rape charges for allegedly having sexual relations with an underage former student during a span of several months this year, in what Suffolk District Attorney Rachael Rollins called “the ultimate betrayal of a child’s trust.”

Manuel Mendes, 38, of Hyde Park, was arrested Friday and appeared Monday in West Roxbury Municipal Court, where he pleaded not guilty to four counts of aggravated rape of a child under the age of 16, officials said.

Bail was set at $35,000 cash. If he posts bail, Mendes must have no contact with the alleged victim and any witnesses, keep away from the Timilty school and any current or former students, have no unsupervised contact with children under 16, and submit to GPS monitoring.

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A lawyer for Mendes declined to comment.

Boston Public Schools officials said they immediately placed Mendes on paid administrative leave after learning about the arrest.

In a statement, they said they are cooperating with police and that the BPS system remains a “safe, welcoming learning environment,” with the top priority being “the safety and well-being of our students and staff.”

Last month, the alleged victim disclosed “multiple assaults” by Mendes, telling investigators in an interview that they had taken place between February and the summer. Electronic evidence, including text messages, was recovered during the probe, prosecutors said.

“As an educator and school official, Mr. Mendes had a duty to provide a safe and supportive environment for this young person to learn and grow,” Rollins said in a statement. “Instead, he allegedly used his position of trust and authority to prey on the victim.”

Rollins urged Timilty parents and guardians to assure their children that they can discuss things that may make them scared or uncomfortable.

“If they raise any issues that cause concern, families in Suffolk County should reach out to my office or our partners in law enforcement or at the Children’s Advocacy Center of Suffolk County,” Rollins said. “There are resources and services available to children and parents.”

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Timilty Middle School has about 300 students in grades six through eight. Mendes earned $99,715 last year in base salary and overtime, according to city records.

Mayor Martin J. Walsh on Monday decried the alleged assaults.

“This is a horrific situation, and these allegations are deeply disturbing and utterly reprehensible,” Walsh said in a statement. “The matter is being thoroughly investigated by the Boston Police Sexual Assault Unit and the Suffolk County District Attorney’s Office, and the victim, who showed incredible bravery in coming forward, will receive every support available.”

Prosecutors had asked that Mendes be held on $100,000 bail, Rollins’s office said. Under state law, prosecutors could not ask Judge Catherine Ham to order Mendes held without bail under the state’s dangerousness statute.

“Despite the egregious nature of the charges against Mr. Mendes, the Supreme Judicial Court has ruled that the offense of statutory rape of a child does not involve the predicate level of force or threat of force necessary to qualify under the dangerousness statute,” prosecutors said. “DA Rollins has repeatedly made clear that she hopes to work with the Legislature to change that.”

Mendes is due back in court on Jan. 15.



John R. Ellement can be reached at john.ellement@globe.com. Follow him on Twitter @JREbosglobe. Travis Andersen can be reached at travis.andersen@globe.com. Follow him on Twitter @TAGlobe.