According to Metro UK, the boy explained to the court how she beckoned him into the cubicle.
She however denies sexual activity with a child under 18 while in a position of trust.
The pupil and the school concerned cannot be identified for legal reasons.
An allegation of the affair only came to light after another male pupil at the school became aware of the relationship and threatened to expose Miss Wilson unless she had sex with him, prosecutor Virginia Cornwall told the court.
She said Miss Wilson, known as Ellie, was a “bright and capable” science teacher who was “highly regarded”.
A “bond” developed between her and the boy on the trip, which took place when she was 26, after “an erosion of boundaries”, Mrs Cornwall said.
On the flight home, the pair were seen by another pupil “sitting inappropriately” after they had been drinking, the jury heard.
Mrs Cornwall said the alcohol led to “a lack of inhibition” and the pair went to the plane toilet together where they had sex.
‘I just sat there for a bit and started to chat to Eleanor. We were sat down and were just talking. ‘She had been drinking and I was drinking some more,’ he told police. ‘She touched me on the arm and I am a little bit shocked and I touched her back.
From there she kissed me on the cheek and then kissed me properly on the lips and I kissed her back and went on from there.
‘There was a lot of body touching and stuff like that. She went to the toilet and from there she called me in. I walked in, closed the door and locked the door.’ The boy told police that the pair then had sexual intercourse in the toilet. ‘It was making a lot of noise because we were banging against the door,’ he said
After the trip they exchanged telephone numbers and met several times.
She later told the boy she was pregnant by him and decided to have an abortion and kept it from her boyfriend.
Mrs Cornwall said:
“There is no doubt there was a pregnancy but she does not accept that she had intercourse with the boy or that he was the father.”
She later informed the school which conducted an investigation and she resigned from her job, the jury heard.
Miss Wilson faces four counts of sexual activity with a child under 18 while in a position of trust.
The case continues.
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