A Long Island principal who boosted graduation rates and test scores claims he was canned because of his speech impediment.

John DeBenedetto, who suffers from a genetic disorder which left him with a malformed upper palate, is suing the Rocky Point School District in Brooklyn federal court for discrimination.

“We accomplished a lot in my three years at Rocky Point [HS]. To find out I was being judged on my disability by the [school] board, and not my performance, is hurtful,” he told The Post.

But just days before a March 2015 vote on whether to grant DeBenedetto, 42, tenure, board president Susan Sullivan allegedly asked, “I can’t even understand him when he speaks. How can he lead the school?”

His lawyer, Joshua Beldner, said, “It’s virtually unprecedented of the board to reject the recommendation of the superintendent.”

The district declined to comment.