The superintendent is being charged with defecating in public, public lewdness and littering.
Tramaglini lives several miles from the school but is superintendent of a different school district, in Kenilworth.
Authorities began hunting for the "mystery pooper" after Holmdel High School staff and coaches for football and track reported finding human feces on or near the field almost every day.
Thomas Tramaglini, 42, is accused of defecating there after he went on his morning jog. The charges were filed Monday, according to published reports.
ABC News was unable to reach Tramaglini for comment.
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The statement added that state law means leave without pay can only be granted in cases of "indictments or tenure charges".
A supintendent at a New Jersey school district was arrested this week for allegedly pooping repeatedly on the football field of a school in another district. Of the more than 20 comments posted about the story on the Asbury Park Press Facebook site, comments mostly focused on the overwhelming power of nature.
"Earlier today, we learned of municipal court charges facing our current superintendent of schools in Holmdel, NJ", said the board.
Tramaglini requested and was granted a paid leave of absence from the Kenilworth School District, where he was "unanimously appointed" to be the superintendent in December 2015, according to the district's website.