The school is located on the shore of Lake Michigan just outside Glen Arbor, with the Crystal River running through the property.

Leelanau for Boys was founded in 1929 by William M. "Skipper" Beals and his wife Cora, née Mautz, faculty members at the upper school of The Principia, in response to the popularity of their summer camp for boys on the same site at the mouth of the Crystal River on Sleeping Bear Bay.

[1] In the beginning, it offered instruction for grades 7-10 only; its first high school class graduated in 1932, with state accreditation following in 1933.

[2] But while the camps—a nearby "sister" camp, Kohahna, for girls, was owned and run by Skipper Beals' sister, Maude Beals Turner—maintain close ties to Christian Science to the present day, the school dropped its official religious denominational focus early on.

In 1944 growing interest in alpine skiing convinced Major Huey to form the Sugar Loaf Winter Sports Club; as the first president of the club, he hired German émigré Hans "Peppi" Teichner to be its manager in 1946.

The school grounds were exempted from eminent domain associated with the formation of Sleeping Bear Dunes National Lakeshore, which surrounds the campus.

Leelanau is by far the smallest school in Michigan ever to place so high in an MHSAA open (unrestricted by enrollment) state championship.