It was founded by Thaddeus Fairbanks, and accepts the majority of its students through one of the nation's oldest voucher systems.

"[4] The school was reincorporated in 1873 in order to accomplish the founders' goal of providing educational opportunities to a wider range for students beyond those destined for the liberal arts colleges and universities.

[3] One of the original buildings contributed by the Fairbanks in 1873, North Hall, burned on March 6, 1956.

The Academy is fully accredited by the New England Association of Schools and Colleges[10] and approved by the Vermont State Department of Education.

The boys' track and field team has won 34 Division I state championships, most recently in 2023.

[12] The girl's indoor track and field team won Division 1 state championships in 2015, 2016, 2017, 2018 and 2019.

The girl's outdoor track and field team won Division 1 state championships in 2015, 2016, 2017, 2018 and 2019.

The boys' ice hockey team won the Vermont State Championships for Division 3 in 1994, 1996, 2001 and 2003.

The center supports programs and activities intended to foster global education aimed not only at the school but at the surrounding community.

[21] The Colwell Center supports language learning, cultural understanding, and travel opportunities for students and faculty.

Every year since 1989, a group of Japanese boys from the Kaijo Junior & Senior High School in Tokyo, Japan have come to St. Johnsbury Academy for a 10-day stay with a student host family.

[23] The center formerly offered an exchange for students go to Stuttgart, Germany for about 5 weeks over their summer break.