Tracing its roots to the Methfessel Institute, which was founded in 1862, the Staten Island Academy and Latin School was officially chartered on September 5, 1884, by a group of prominent educators who facilitated the merger with the Institute. Anton Methfessel, the Methfessel Institute’s founder and Headmaster, was a distinguished teacher and proponent of language education, and he served as a member of the Board of Trustees of the newly organized school.

The Academy rapidly expanded, dropped the phrase “Latin School” from its name, and gained national prominence with a curriculum that was progressive for its day. In 1885, required courses for the Intermediate Form (Grades 9-12) included Latin, German, French, English, geography, physiology, zoology, mathematics, history, natural philosophy, expression, music, and drawing. The Academic Form required more advanced study, and The Latin School division mandated, additionally, student literacy in both Latin and Greek. Many prominent professionals in theater, education, literature, politics and business were associated with the Academy throughout this period including actor Sidney Wollett, North Pole explorer Admiral Peary, Booker T. Washington, the Vanderbilt family, Jacob Riis, and George William Curtis, a member of the Academy’s Board of Trustees and the namesake for Curtis High School.

In 1891, the school bought land at the corner of Wall Street and Academy Place, a street that was named after the school, in the St. George section of Staten Island. Because of the expanding student population, a grand new building of English architectural design was built, and the cornerstone was laid in December of 1895. That historic cornerstone now stands outside Alumni Hall on the school’s Todt Hill campus.

At the turn of the century, the Academy made great strides, and its stature in educational circles expanded. The school explored and adopted "new" educational pedagogies, including those espoused by John Dewey and Friedrich Froebel, the creator of the Kindergarten. Athletics gained prominence as interest in facilitating a connection between physical education and intellectual growth emerged, and the Academy expanded its athletics offerings. Teams during the early part of the 1900's included football, ice hockey (played at Silver Lake), track and cross-country running, basketball, baseball, tennis, and shell-racing. The growing program forced Academy athletes in 1921 to hold their contests at fields that had been given to the school on Delafield Square.

In 1931, a field house and additional athletic fields were acquired when the school purchased land off Todt Hill Road, and Staten Island Academy donated the land at Delafield Square to the City of New York, which created Walker Park from it. During this time, William Winter, a famous critic and patron of the arts, established the Winter Memorial Library at the school in honor of his son Arthur, an Academy student who had died while he was enrolled at the school. Through Mr. Winter's influence, the collection of the library, which was modeled after Sir Walter Scott’s, included autographed portraits of Dickens, Gladstone, and Disraeli. Its shelves held first editions of Twain, Dickens, Johnson, Byron, Andrew Carnegie, and Bram Stoker, as well as other rare books and prints. The library was heralded as the best secondary school classical library in the nation.

During and after the Depression years, the Academy acquired and merged with several other private schools, including the Livingston School, a highly regarded progressive elementary institution, the Dongan-Hall Arden School, which was located on the present day Todt Hill Campus, and the Willard-Mundorf School.

In the 1940's, the Lower and Middle Schools of the Academy moved to Dongan Hall, a Georgian mansion that was formerly the estate of Edward Stettinius, FDR’s and Truman’s Secretary of State. The Upper School remained at the Wall Street campus.

The Academy maintained two campuses for many years. On December 10, 1964, ground was broken on the Todt Hill campus to build facilities to house the entire school. The Todt Hill campus additions included structures still in use today -- the Early Childhood Building, Kearns Hall, and the O.J. Buck Gymnasium.

Alumni Hall was completed in 1970, and the entire student body was accommodated on the beautiful Todt Hill campus shortly thereafter.

In September 1975, tragedy struck, and a fire destroyed Dongan Hall, the jewel of the Todt Hill campus. The building's structure was irreparably damaged, and most of the Winter Memorial Library portrait and book collections was lost. A single remnant from Dongan Hall, a pendulum clock, was saved.

The clock now hangs in Crowe Hall, which was built in 1976 on the site of the historic Dongan Hall building. Crowe Hall contains the Patrick Commons (the dining hall), the Head of School's office, and other administrative spaces. Haugen Hall, which houses the auditorium, Stanley Library, and arts classrooms, was also built in 1976.

The Academy continues to expand to meet the ever-changing needs of students. In 1995, the Francis H. Powers Science and Technology Center was added to Kearns Hall. Campus facilities also include two outdoor swimming pools, tennis courts, athletic fields, and the romantic Art Barn, which is the last remaining original structure on the campus and is used for Lower School students’ art classes.

In the summer of 2003, the Academy continued to enhance the facilities. The Stanley Library was entirely renovated, the Patrick Commons dining hall was upgraded and new playground equipment was installed. A fitness center opened in the fall of 2003 thanks to the generosity of the Parents' League.

The Academy broke ground for the restoration of the school's athletics fields in the summer 2004, . The Alexander Robbins Steinman Foundation generously funded the project in honor of Alex, class of 1986, who died on September 11.

A Memorial Fund dedicated to Nancy B. Avis, a 1986 Advance Woman of Achievement and ardent supporter of the Academy's sports teams, made possible a number of major improvements to the O. J. Buck Gymnasium. The benefits from the fund included refurbishment of the school's training room and the gymnasium floor, new electrically operated folding bleachers, and a rock climbing wall. Our data center was also virtualized this year and all of the switches and fiber runs to buildings were also upgraded to increase processing power and expansion capabilities. This upgrade promotes “green computing” by reducing energy consumption and cooling requirements.

The PARC, which stands for Patrick Academic Resource Center, opened its doors to students from all three divisions in September 2013. This new study space, which occupies two classrooms on the bottom floor of Alumni Hall, is equipped with supplies, laptops, iPads, printers and SMART boards.

On May 30, 2015 Staten Island Academy dedicated a memorial arboretum to NYPD Officers Rafael Ramos and Wenjian Liu who were tragically killed in the line of duty. Officer Ramos' son Justin graduated from the Academy in 2013. Members of the Class of 2013, 2014, and 2015 contributed significantly to the funding of the memorial.