[2] In 1858, John McMahon and Vincent Hayes, Franciscan priests from the Roundstone Monastery in Ireland came to the United States to begin work on establishing an academy dedicated to educating underprivileged youth in the Brooklyn diocese.

[5][6] St. Francis Academy opened in a building on 300 Baltic Street in Cobble Hill, Brooklyn, with 30 students and six Franciscan priests.

The academy expanded and grew to encompass six row houses, with 150 feet (46 m) of frontage, and a former Methodist Church on Baltic Street.

By 1917, the college's enrollment dropped to half, due to students enlisting in the military as the United States entered World War I.

In 1926, the Franciscan Brothers opened a new facility on Butler Street, after raising US$250,000 through a fundraising campaign dubbed the "Great Drive.

Most of those still enrolled were members of the Franciscan order and those exempt from military service (12 SFC students gave their lives to the war effort).

[4] In 1957, the Regents of the University of the State of New York granted an absolute charter to the trustees of the college, making it a separate legal entity from the St. Francis Monastery.

[12][13] In 1969, the college became a co-educational institution, and additional property was purchased on both Remsen and Joralemon Streets, allowing enrollment to exceed 3,000 students.

In fall 2005, the 35,000-square-foot (3,300 m2) Frank and Mary Macchiarola Academic Center opened, which included the new St. Francis College Library, classrooms equipped with wireless internet access, smart boards, and multimedia technology, a theater/lecture hall, updated facilities for the Communication Arts department, gathering spaces such as a lounge with Wi-Fi for students, and office space for several academic departments.

Affiliation agreements with the SUNY Downstate Medical Center, New York University College of Dentistry, and New York College of Podiatric Medicine enable students to pursue degrees toward becoming physician assistants, radiologists, and physical or occupational therapists and to acquire advanced standing in professional programs in dentistry and podiatry before the completion of the baccalaureate degree.

For students who excel academically and participate in extracurricular activities that embody the "Franciscan spirit," St. Francis College established the Duns Scotus Honor Society.

Members of the institute have engaged in a series of research projects, edited books, sponsored conferences, and introduced novel curriculum development.

[24] The institute has supported the writing and editing of numerous publications in international psychology, including 17 books in five countries.

[25] The Center of Excellence in Project Management launched in 2011[26] and held its first annual Practical Research Forum on June 6, 2011, a series of lectures combining academic theory and real-world project-management experiences.

[34][35] From 2014 to the present, St. Francis College has been ranked by Money magazine in quality of education, affordability, and outcomes for students.

The St. Francis College men's basketball team, founded in 1896, was the oldest collegiate program in New York City.

The Terrier's had their best season in 1955–56 under head coach Daniel Lynch, they posted a 21–4 record that ranked them 13th nationally in the AP polls and reached the NIT semi-finals.

[41] Then, during Ron Ganulin's tenure as head coach in the late 1990s and early 2000s, the team was one of the best in the NEC; from 1998 through 2004, St. Francis posted a 78–36 conference record.

The Terrier's had their best season in 2014–15 under John Thurston by winning the NEC Tournament Championship and receiving the program's first NCAA bid.

In 2012, the men's water polo team won the Eastern Championship for the third time in the program's history and earned an NCAA Final Four berth.

[46] In 2013, the Terriers won the Eastern Championship for the fourth time in the program's history and earned an NCAA Final Four berth, finishing 4th.

The Aquatic Center's pool was used to film scenes for the movie Across the Universe (2007) and the HBO comedy series Flight of the Conchords.

[49] The Thomas J. and Anita Volpe Lounge was used by the popular TV show Gossip Girl to film scenes for Season 4, Episode 10: Gaslit.