Bristol Crown Court heard how she was perched on one leg in the cramped toilet while they had full intercourse.
Their relationship was exposed when a jealous friend of the victim tried to blackmail her into having sex with him.
In a police interview played to the court, the boy said: “She ran her hand around my penis. I was wearing jogging bottoms. I carried on and then she slid her hand down my boxers, there was a little foreplay.

Teacher Eleanor Wilson outside Bristol crown court, where she is on trial accused of sexual activity with a pupil

The science teacher allegedly had sex with a teenage pupil in the toilet of a plane as they returned from a school trip, a court has heard.
Eleanor Wilson, 29, is accused of touching the boy as she sat next to him on the flight before beckoning him into the toilet and performing oral sex on him. They then had full sex in the cubicle, court documents state.
Bristol crown court heard that Wilson later told the boy she was pregnant and he was the father, but that she would have an abortion.

Prior to the allegations the science teacher was deemed a bright and capable teacher. With her reputation now in tatters, Eleanor Wilson [left], marches toward the Bristol Crown Court where her trial for sexual exploitation of a minor is being heard

“That went on for a bit. Then she proceeded to go into the toilet. She called me in. I walked in closed the door and locked the door.
“We proceeded to kissing and touching and at this point she had my hand down her boxers.
“From there, she pulled down my jogging bottoms and she was placed on her knees.
“My back was against the wall and she was knelt in front of me. Then when she stood up my trousers were down anyway and she pulled her trousers down.
“It became difficult it wasn’t working – she’s very tall.”
After they had full sex the boy recalls having a “very brief conversation” with her on how they were going to get out of the toilet.

The inappropriate contact between Wilson [left] and her pupil was exposed when a jealous friend of the student’s tried to blackmail the her into having sex with him, as the price for keeping mum about the relationship

Long after the trip, the pair exchanged telephone numbers and even had a reunion meal at a restaurant, where he gave her flowers and chocolate.
After returning home, their “clandestine” relationship continued, with Wilson and the teenager going for a meal at Nando’s with others from the trip, the jury was told.
They also allegedly had days out together at Tintern Abbey in Monmouthshire and Ashton Court near Bristol, went for pub meals and drank pints of cider together.
The court heard that the boy bought Wilson flowers and chocolates and showed her his bedroom, where they kissed.
Virginia Cornwall, prosecuting, told the court how the pair became close during the outdoor camping holiday to Africa.
They would ‘pair up’ for activities and stay up late talking after other teachers and pupils had gone to bed, which led to an “erosion of boundaries”.
A month later, at school, Wilson told the boy that she was pregnant, and he could be the father but that she would get an abortion, the court heard.

Wilson, a science teacher and head of Key Stage Four at the high school, has in Bristol been described as a ‘risk taker’ – According to the prosecutor, “Such intimacies and attraction built up during the days and nights of the trip, which resulted in close contact on the plane.”

Prosecutor Virginia Cornwall,  described Eleanor Wilson as a bright and capable teacher but a risk taker. She said that during the overseas trip Wilson and the boy, who cannot be identified, spent a lot of time together.
“It was the circumstances in which the two interacted on that trip that led to an erosion of boundaries and it was her responsibility, the crown says, as the adult, to ensure there was no erosion of boundaries,” she said.
“She was a 26-year-old woman and he was a teenage boy. It was her choice to be with him. There were a lot of nighttime chats where others had gone off to bed. He was being treated on a par, an equal basis, as if an adult.”
Cornwall said Wilson and the boy had been drinking on the flight home. “It was the alcohol, you might find on the evidence, contributed to the lack of inhibition on the part of the defendant,” the prosecutor said.
“Such intimacies and attraction built up during the days and nights of the trip, which resulted in close contact on the plane.”
Wilson beckoned him into the toilet, where they had sex, Cornwall said. “Having had sex they went back to their seats. It was a secret between them.”

Wilson [left], allegedly performed foreplay on the boy in their plane seats and then led him into the toilet where she gave him oral sex, than full intercourse while perched on one leg

Wilson [photo], had a boyfriend when she allegedly had sex with her 16-year-old pupil in Aug 2015

Disgraced high school science teacher Eleanor Wilson [photo], has pled not guilty to four charges of abuse of position and sexual activity with a child

The relationship was exposed when another pupil tried to blackmail her.
Ms Cornwall said: “Another pupil became aware of what had happened and started emailing Ms Wilson threatening to expose her unless she in turn said she would have sex with him.
“She engaged with this blackmailer. Instead of going immediately to a superior she tried to deal with it herself.
Ms Cornwall said: “She was a woman having a clandestine relationship with a boy.
“She is a risk taker. She does accept there was inappropriate conduct outside of school, but nothing sexual.”
She added: “He is a young man who has no motive for making all this up.”
The boy’s dad reportedly thought Wilson was supporting his son, who had just broken up with his girlfriend.
Wilson, of Dursley, Gloucestershire, denies four charges of sexual activity with a child by a person in a position of trust, claiming the boy’s version of events was a “distorted fantasy”.
Wilson, a physics teacher, was head of Key Stage Four at a Bristol secondary school when the alleged offences took place three years ago.
Wilson has been struck off on recommendation from the National College for Teaching and Leadership.
The trial continues.