St. Thomas Academy announced the departure of headmaster Matthew Mohs on Tuesday and said it was effective that same day.
Mohs, a 1990 graduate of the all-boys Catholic military school in Mendota Heights, had been headmaster for nearly five years.
The school's board announced that Mohs' resignation "was a deeply personal decision."
"I hope you will support him as he transitions to the next phase of his career," the notice said.
A message was left Thursday afternoon with Mohs seeking further details about his resignation.
The school's board of directors said it will appoint an interim headmaster while the search for a permanent replacement is conducted.
Mohs, 47, became headmaster in July 2014 after serving as chief academic officer for the St. Paul Public Schools.
Mohs received a bachelor's degree from the University of Notre Dame and master's degrees from the University of Portland in teaching and public administration from the University of Minnesota's Hubert H. Humphrey Institute of Public Affairs.
For the 2017-18 school year, St. Thomas had 632 students in grades 6 through 12.