A Brooklyn special-ed teacher was arrested yesterday for roughing up a 10-year-old boy — the second time in eight years that he’s manhandled a kid left in his care, authorities said.

Gary Smith, 60, was charged with assault, harassment and endangering the welfare of a child.

Sources said that when the special-ed pupil at PS 92 in Prospect-Lefferts Gardens refused to obey an order to pick up a hat he had dropped, Smith allegedly grabbed him by the neck and threw him down. An assistant principal called police, and the boy was treated for nonserious injuries at Downstate Medical Center.

“There was a similar incident in 2003, and [Smith] was disciplined, reprimanded,” said Department of Education spokeswoman Margie Feinberg.

Smith, at PS 92 seven years, has taught special ed since 2000.

Meanwhile, Bronx middle school staffer Isaac Bowens, 39, was busted yesterday for allegedly showing porn to a 15-year-old at MS 219. He was charged with harassment, disseminating indecent material and endangering the welfare of a minor.