She was found guilty of having sex with the boy, performing oral sex on him and kissing him.
The jury found her not guilty on two charges of doing an indecent act on a child.
The teacher gasped and cried as the verdicts of "guilty" were read out.
Some people gathered in the public gallery also cried as the jury announced its verdict.
Outside court, one of the boy's relatives said the family was glad the trial was over.
"Of course we're relieved," she said.
The alleged offences happened in and around Porirua and Paraparaumu, north of Wellington.
The boy, now in his mid-teens, told the court about a visit the pair made to a motel in early 2014.
The court heard the Wellington woman became pregnant after the visit, but had an abortion.
But the woman denied claims of sexual offending against the boy.
"It's disturbing. It wasn't me. I did not do that at all," she said in evidence to the court.
"I would never do that to a child. Never," she added tearily.
During frequently tense cross-examination, she told Crown prosecutor Dale La Hood the boy was a liar and "manipulator", and denied being in love with the boy.
He was "emotionally fragile", she said, but disputed the Crown prosecutor's suggestion this may have made the boy prone to manipulation.
He was "quite street-smart" and was himself "a manipulator of a lot of situations", the teacher claimed.
She initially faced 15 charges, and was accused of kissing the boy and having oral sex between 2011 and 2014, as well as one instance of sexual intercourse.
The woman's name suppression will be reviewed on November 6.
She will be remanded in custody ahead of her sentencing on Friday November 27.
- additional reporting: Jimmy Ellingham of NZME News Service
