In 1906, a group of Presbyterian ministers and laymen began an enterprise to form an annual series of summer Bible conferences in the tri-state area of New York, New Jersey, and Connecticut.

After having visited the hamlet of Stony Brook in 1907, Carson and his associates settled on a location directly across from the train station.

Carson's vision also included the establishment of a boys' school which could use the Assembly grounds outside of the summer months.

Stony Brook’s prime reason for existence has been to bring its [students] into vital contact with the Christian faith.”[6] The academic reputation of the school grew in prominence.

The school offers twenty-one Advanced Placement (AP) courses as well as numerous full-year elective courses in such subjects as the Engineering, Innovation, and Design (STEM), History of Philosophy, Ethics and Politics, Advanced Digital Imaging, and 20th Century Fiction and Creative Writing.

Students also have opportunities to take mini-courses interspersed throughout the year in a wide range of electives as well as conduct various internships and research opportunities off-campus at nearby institutions such as Stony Brook University, Brookhaven National Laboratory, and Cold Spring Harbor Laboratory.

From 1974-2018, Stony Brook was a member of Section XI of the New York State Public High School Athletic Association.