Travis County Jail records show Holly Marie Lopez of Pflugerville was in custody Friday on charges of aggravated sexual assault.
Bond is $100,000 for Lopez, who was booked Thursday. Online jail records did not list an attorney for her.
Officials say Lopez allegedly gave condoms to the 13-year-old and 14-year-old boys and had sex with them at the older child's home on Feb. 11.
The Lexington Independent School District says Lopez was put on administrative leave about two weeks ago when the allegations became public. Supt. Frances McArthur says Lopez later resigned.
Lopez was special education math teacher in Lexington, located 50 miles east of Austin.