Prosecutors have charged Pete Hernandez with three counts of indecency with a child. He no longer works for the district, HISD said.
The district said allegations were reported in November, and HISD promptly removed Hernandez from the campus of Looscan Elementary School in Near Northside, and also notified Children's Protective Services.
"HISD takes situations such as this very seriously, as the safety of students is always the district's top priority," HISD said in a statement.
A LinkedIn page for Hernandez stated he began working at HISD in September 2015. A search of Harris County criminal court records does not reveal any previous convictions for Hernandez.
Hernandez is far from the first HISD teacher to be accused of a sex crime in recent months.