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Chevalier, who is believed to be unmarried, now faces charges including unlawful sexual activity with a child and transmission of harmful material to a child.
She has not yet entered a plea and is awaiting her next court date.
Between September and November 2016, the pair met up in the school kitchen where he touched her bare vagina and where she 'rubbed' his genitals over his clothes, police say.
It is the second child sex abuse scandal to hit the religious school this year.
In May, the former principal's husband Bruce Mc Allister was accused of molesting foreign exchange students who were visiting the academy.
Haughey was also branded 'disingenuous' and told she presented a 'significant risk' of sexual offending towards teenagers known to her.
She must have no contact with the boy, his family or children under 16, not use social media without permission and not delete her internet history.