The incident involves a female eighth-grade teacher at Memorial Middle School.
The school district's superintendent identified the teacher as Kathryn Camille Murray. She has been charged with sexual assault of a child, and school officials are working with law enforcement to investigate the allegations.
The district became aware of the alleged relationship after a faculty member reported it to the school principal on February 13. She was removed as teacher that same day.
The school district didn't disclose the age and grade of the student nor whether he was in any of Murray's classes.
The district say it's reported the allegations local Children's Protective Services, the Spring Branch ISD Police Department, and the State Board for Educator Certification. The SBISD Police Department is continuing to investigate.
The district says counselors will be on hand to provide any help in the days ahead.
In a statement issued Thursday evening, the school district wrote: "The safety of every SBISD student is our very highest priority. We are deeply shocked and outraged by this alleged conduct. We will never tolerate any teacher or other employee who takes advantage of and harms a student. This allegation, if true, represents a complete breach of the trust that our children and our community place in our educators every day. We are saddened by these allegations, and we are very concerned about the well-being of the student and his family."
Anyone with information is asked to contact the SBISD Police Department at 713-984-9805.
