Bernadette Smith, 35, had quit her job as a history and English teacher at Bannockburn High School on Friday after allegations arose that she had a relationship with a 16 year old student.
The married mum of three was called in to a meeting with head teacher Tom Black at the school on Friday before resigning her post.
However it emerged today that she has now retracted that decision after speaking to her union.
Smith was held by cops last weekend over the claims, part of which allege her and the pupil engaging in activity in a public park.
She appeared in court on Monday morning to deny the charges against her.
Taken to and from court in the back of a police van she appeared looking stressed and tired.
She denied the single charge that between September 13 and 20 this year at an address in Cowie and at Callander Park, Falkirk, that while being a person who has obtained the age of 18 and was in a position of trust, namely that she was the boys teacher, did engage in sexual activity with or directed towards the pupil in that she did kiss him on the mouth and neck and lie beside him on a bed while partially clothed.
She then met with representatives from the Educational Institute of Scotland, who advised her not to make her resignation official in writing - meaning she is still a member of staff at the high school.
A spokesperson from Stirling Council said: “The EIS have been in touch with the school to advise them that Bernadette Smith has retracted her resignation, which has implications for ongoing processes within the council.
“If she’s still an employee, there are investigative processes we have to go through.
“The staff, the headteacher and his management team at Bannockburn High have done a huge amount of work to deal with this matter as properly and as quickly as possible, putting the young person’s wellbeing at the forefront.
“But we are now also talking about someone who has employment rights, and we need to bear that in mind now.”
Parents of pupils have also criticised education bosses after hearing of the scandal in the media before they were told by the school.
Headteacher Mr Black sent text messages and letters to parents on Monday afternoon, after a weekend of newspaper coverage and Smith’s appearance in court.
Councillor Alasdair MacPherson said: “I had a call on Sunday from a parent who had opened the newspapers to be confronted with this story, after the school had refused to say anything.
“Their concern was that the children all knew about it, and they felt the school had a duty to give parents some information so they could be prepared. But the school refused to confirm or deny anything.
“Everybody is well aware there’s a sensitivity about this, but the lack of communication with parents and the complete shutdown by senior management is a disgrace.”
One mum said: “It’s just laughable that this story is splashed across the newspapers and the internet before the school pays us the courtesy of telling us what’s going on.
“We entrust our kids to their care and deserve to be warned of something like this.
“I have had to talk to my child about this issue and would have like to have been prepared instead of getting totally blindsided by this scandal through media reports.”