The college has been named by U.S. News & World Report as one of the "Best Regional Colleges in the South" (#2 in 2018 and 2017) and in The Princeton Review "Best 380 Colleges." Its 2015–16 tuition was $16,830 (excluding room and board) and its acceptance rate averages 40% of its annual applications. The college had an endowment of over $60 million as of April 2011.
Founded in 1968, the campus comprises 19 acres (77,000 m2), the centerpiece of which is the Ponce de León Hotel, built in 1888 as a luxury hotel. The architects were John Carrere and Thomas Hastings, working for Henry Morrison Flagler, the industrialist, oil magnate and railroad pioneer. It is now listed on the National Register of Historic Places.
Lawrence Lewis, Jr., was the driving force behind Flagler's development. It was his vision to create a small, private liberal arts college on the old hotel grounds. Lewis was Chairman of Flagler's Board of Trustees for more than 20 years, guiding the college through a reorganization in 1971. He directed millions of dollars through foundations, family and personal funds into new construction, restoration projects, endowment and various other programs to ensure Flager's continued success. Lewis was related to Henry Flagler through his mother, Louise Wise Lewis Francis, who was the niece of Mary Lily Kenan Flagler, who married Henry Flagler in 1901 making him Lewis' great uncle. 
In 2014, Flagler College was ranked eighth among Regional Colleges in the South according to the U.S. News & World Report college survey. But in February 2014 the college's vice president of enrollment management resigned after it was determined that he had been altering student test scores, GPAs, and student rankings to enhance the college's image, standing, and reputation. The college hired a Jacksonville law firm to investigate. The report indicated that the college had been reporting false information since 2004 to various organizations, including the U.S. Department of Education and various ranking organizations.
The Proctor Library, in the northwest corner of campus, is Flagler's sole library facility. It is named after William L. Proctor, Flagler's chancellor, who was president of the college from 1971 until 2001. Like many of the historic buildings on campus, the Proctor Library's architectural design reflects the Gilded Age style popular during the time of Henry Flagler's construction of the Ponce de León Hotel in 1888. The Proctor Library was built in 1996.
The Proctor Library has a plethora of services and modern technology available to suit its large and diverse body of patrons and their research needs. Services include access to the library's collection, general reference and research assistance, an interlibrary loan program, four large group collaboration areas, nine group study rooms, and seating for up to 500 visitors. Other features include a sizable open-access computer lab, four technology-equipped classrooms, and a graphic design studio, all on the third floor. The library's collection contains approximately 102,047 printed volumes, 212,689 electronic books, 4180 audiovisual items, 630 periodicals, and 5 newspapers, as well as almost 44,000 full-text electronic periodicals and 50 online databases.
Modern technology available at the Proctor Library includes 200 computer workstations, available to Flagler students, faculty and staff, and advanced audiovisual and computer projection capabilities in the large group collaboration areas. The library also has several accessibility-forward features for those with reduced vision or hearing capabilities. The proximity of the Florida School for the Deaf and Blind makes this technology especially valuable. This specialized technology includes the JAWS (screen reader) program, a CC-TV with the ability to enlarge print for reading, a Sara Ce scanning and reading device, and a specialized workstation that offers Connect Outloud and OpenBook accessibility software.
Flagler offers membership in nine honor societies, including Alpha Chi, Alpha Psi Omega, Kappa Delta Pi, Omicron Delta Kappa, Phi Alpha Theta, Psi Chi, Alpha Kappa Delta, Sigma Tau Delta, and Phi Alpha Delta. In addition, there are over 55 active student clubs and academic organizations on campus.
Flagler competes in 14 varsity sports (basketball, cheerleading, cross country, golf, soccer, and tennis for men and women, baseball for men only, and volleyball and softball for women only) in Division II that compete in the NCAA. Its teams are called the Saints. In the 2009–10 season Flagler athletics began to play in the Peach Belt Conference. In 2009 the Flagler College Lady Saints volleyball team made it to the national championship, and finished in the top four of Division II volleyball teams in the nation. In 2010, the Lady Saints made it to the regional finals, finishing top 16 in the nation.
The Gargoyle is the college's student-run newspaper. In 2010, it went online-only. At the 2012 Society of Professional Journalists’ Mark of Excellence Region 3 awards, The Gargoyle took first place for best independent online publication and first places for editor Michael Newberger in online opinion writing and sports editor Mari Pothier in online sports reporting.
Since becoming online-only, The Gargoyle has won nine Regional Mark of Excellence awards and published three more from Flagler Communication Department classes. Before 2010, the publication had only won two SPJ awards in its history. In 2007, the publication was a finalist in the Associated Collegiate Press Pacemaker Awards.
In 2006 and 2007, there were several allegations of censorship or alteration of articles in the Gargoyle by the college administration. In 2006, one issue of the newspaper was removed from circulation due to an alleged error in its headlines about rising tuition. In April 2007, the college administration again exercised editorial control over the paper due to alleged factual errors. Students rallied and organized a protest against any type of censorship of the newspaper, calling for a free and independent student press.
After September 2007, working on The Gargoyle was no longer required of communication majors. An advisory board and operating guidelines were set up for The Gargoyle.
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