The founder of a Brooklyn high school and two-time City Council candidate is under investigation for allegedly engaging in sexual misconduct with a female student.

Juan Martinez — president of Progress Inc., the nonprofit that started Progress HS for Professional Careers in Williamsburg — is the third male worker at the school to be accused of inappropriate conduct with a student since 2010.

City Education Department officials confirmed that Martinez, 50, who works out of a Progress Inc. office at the school, is barred from the grounds pending an investigation.