Officers arrested James Wilder, 47, at Sperring Middle School on Tuesday morning. Wilder also coaches cross country and track at Lindbergh High School, where the then 16-year-old victim was a student and athlete.
"We are troubled and disturbed when we receive allegations such as this," a Lindbergh School District spokesperson told reporters. "We want our parents to know we'll do whatever we can to cooperate with police."
The victim came forward this summer, telling police that she and Wilder had an ongoing sexual relationship from August 1, 1996 until September 21, 1997.
Wilder, now on paid administrative leave, was also arrested back in 2008 for an alleged incident with another female student. Police at the time determined that there was no "credible evidence" indicating wrongdoing.