A 14-year-old special-needs girl was sexually assaulted by a boy when a matron left them unsupervised on an overcrowded school bus in December 2011, the girl’s mother alleges.

The New York City public-school student, whose name is being withheld by The Post, was traveling home from an upstate school Dec. 6 when “she was caused to sustain severe permanent personal injuries when a co-student . . . sexually assaulted” her, according to Manhattan Supreme Court papers filed this week.