"In line with the diligence and impartiality with which I have always performed my duties, I have chosen to resign," she said in a statement.
The Italian Mogherini is accused of abusing her position and rigging procurements to benefit the school, the prestigious diplomatic university College of Europe. The school is funded by the EU and many students from there go on to work in the EU's foreign service.
Between 2014 and 2019, Mogherini was the EU's foreign policy chief and one of the union's highest-ranking politicians. The following year, she got a job as principal at the school.
Mogherini was arrested on Tuesday, along with two others, in connection with dawn raids on the school's campus in Bruges and the EU External Action Service premises in Brussels.
