Florida Atlantic University has been providing higher education opportunities to residents in the northern part of its service area for several decades. Prior to 1993-94 college credit classes were offered at off campus "centers" through FAU's Division of Continuing Education. In northern Palm Beach County, classes were offered at the West Palm Beach Center at 45th Street. When FAU began offering courses at Palm Beach Community College's Eissey Campus, the center became known as the North Palm Beach Center. Moving in 1991 to Dwyer High School, the Center offered a limited number of undergraduate programs in general management, elementary education and public administration, graduate programs in business administration, public administration, educational administration and supervision, and core courses in the graduate nursing program. Fewer than 800 students were enrolled in 55 evening classes. Having virtually no office space, there were only a handful of permanent faculty assigned to the center; instead, faculty traveled north from the Boca Raton Campus to teach these courses

In response, ground was broken to form a permanent northern Palm Beach County campus in Jupiter at Donald Ross Road, and in Fall 1999 the John D. MacArthur Campus opened on 135 acres of land donated by the John D. and Catherine T. MacArthur Foundation. With three administrative buildings, one residence hall, a dining hall and a utility building, the campus welcomed seventy-four Honors College students, who joined 1700 commuter students. Recreational facilities were developed and included a swimming pool, soccer field, basketball court and handball courts.

The Jupiter campus continues to offer a wide variety of courses from seven of FAU’s colleges.

In Jupiter, a second residence hall opened in Fall 2001, the dining hall was expanded and two new buildings, the Hibel Museum of Art and Edna Hibel Fine Arts building were completed in Summer 2002. In the summer of 2004, the Education Classroom building and the 20,000-square-foot Library opened. The previous library site was renovated and became The Burrow, the campus union. The Burrow houses Student Government offices and various student activity equipment, along with the Bookstore and University Police headquarters.

In 2005, FAU Jupiter welcomed Scripps Florida faculty and staff to the first of two state-of-the-art research buildings which served as temporary space while their permanent facility was constructed. In the same year, the three-building Elinor Bernon Rosenthal Lifelong Society Complex was completed, with major gifts from the Rosenthal, Milton Maltz and Pearl Perloff families. On its 10th anniversary in 2009, the Jupiter Campus occupied approximately 45 acres with eighteen buildings totaling more than 333,000 square feet: eight classroom/office buildings, a library, a 500-seat auditorium, two residence halls, a dining hall, a museum building and central utility plant. Recreational facilities include a soccer field, swimming pool, disc golf course, and tennis, volleyball and basketball courts.

In February 2009, leaders from The Scripps Research Institute were joined by Florida Governor Charlie Crist and Palm Beach County commissioners to cut the ribbon officially opening Scripps Florida, the institute's 350,000-square-foot, state-of-the-art biomedical research facility at FAU Jupiter.

Later that year, in October 2009, The Max Planck Florida Institute finalized an agreement with FAU for a six-acre parcel of vacant land adjacent to Scripps Florida to build a 100,000-square-foot biomedical facility and laboratories. MPFI faculty and staff utilized the science buildings originally constructed as temporary space for Scripps Florida before moving into their permanent facility in June 2012.

Students and faculty on the Jupiter campus will be moving into two highly sophisticated laboratory facilities that were originally built for Scripps Florida and the Max Planck Florida Institute. These buildings have been renovated and will host a major new FAU neuroscience institute beginning in January 2013. This continues the development of the Jupiter campus as a flourishing center of biomedical research and education.

The Northern Campuses of FAU continue to be an integral part of higher education in northern Palm Beach, Martin, St. Lucie, Indian River and Okeechobee counties.