Detectives arrested the 30-year-old woman at a school in southwest Sydney after investigating reports a 17-year-old boy had allegedly been sexually touched by a teacher.
She faced Liverpool Local Court on Wednesday, where she was granted conditional bail after being held in custody overnight.
The teacher was given permission to attend via video link when the case returns to court in October.
The woman was earlier charged with sexually touching a person aged between 17 and 18 under special care, sexual intercourse with a person between the same ages while under special care and aggravated sexual assault where the victim was under the authority of the offender.
The NSW Education Department said the teacher had been suspended without pay and support was being provided to students and staff.
"The safety and welfare of students are our highest priorities," a department spokesman said.
"The department has strong policies and procedures in place to ensure their care and protection and to act when employees are alleged to have engaged in misconduct."
The woman is banned from educational facilities as a condition of her bail.
Lifeline 13 11 14
Kids Helpline 1800 55 1800 (for people aged 5 to 25)
1800 RESPECT (1800 737 732)
National Sexual Abuse and Redress Support Service 1800 211 028
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