The court heard that she was subsequently bailed on condition she have no unsupervised contact with anyone aged under 18.
Prosecuting Joe Allman said Boy A went on to attend court and answer questions from Joynes’s barrister in a recorded cross-examination.
Mr Allman added: “The case was then adjourned to await the rest of the trial, but in the meantime it turned out that Ms Joynes had been in a fairly long-term sexual relationship with another of her 15-year-old pupils.
“In due course (Boy B) gave his own account.
“He said Ms Joynes was his teacher, that they were in contact while she was suspended, and that he went to her flat when he was 15.
“They kissed and then, after he turned 16, they struck up a full sexual relationship from she which ended up pregnant.
“So remarkably and, in all honesty quite brazenly, this was all happening while Ms Joynes was on bail to this court.
“Of course she can’t deny that sexual relationship because she became pregnant with (Boy B’s) child and she had (Boy B’s) child.
“Instead, this time she claims the sexual activity didn’t start until he was over 16 and she had been finally dismissed from the school.”
The court heard she had told the boy she was unable to conceive.
Joynes denies two counts of sexual activity with Boy A, two counts of sexual activity with Boy B, and two counts of sexual activity with Boy B while being a person in a position of trust.
The trial continues.
