The investigation by the Pittsburg High School publication, the Booster Redux, started as an introductory profile of the new head.
But after three weeks they found that a college attended by Amy Robertson lacked accreditation.
The six-student news team has drawn praise from journalists around the US.
Ms Roberston was hired by the Pittsburg Board of Education on 6 March.
The school district met on Tuesday night to accept her resignation from the $93,000-a-year (£74,500) post.
