Jacksonville University comprises 6 colleges:
- College of Arts and Sciences: This is the core of the university in the humanities. It includes the School of Social Sciences and Education and the School of Science and Mathematics. The college offers a broad educational experience encompassing quantitative analysis, the scientific method, historical and philosophical perspectives, social sciences, foreign languages, and more.
- Davis College of Business and Technology: This college includes the School of Business, the School of Engineering and Technology, and the School of Aviation and Military Science. Davis College of Business and Technology prepares students to enter the dynamic and complex world of business.
- Linda Berry Stein College of Fine Arts and Humanities: This college aims to provide individualized instruction and guidance to unlock each student's artistic and intellectual potential. It includes the School of Performing Arts, the School of Art and Design, and the School of Humanities.
- Brooks Rehabilitation College of Healthcare Sciences: It includes the Keigwin School of Nursing, the School of Orthodontics, and the newly established School of Applied Health Sciences.
- Law School: Through a unique partnership with the city of Jacksonville, the law school became the first law school in Jacksonville in over twenty years. Located in the heart of the city, students immerse themselves in a dynamic legal community.
- Lake Erie College of Osteopathic Medicine (LECOM) at Jacksonville University: This college offers the region's first four-year medical school, situated on JU's Arlington campus.
Additionally, the university includes various institutes and organizations:
- Public Policy Institute: It offers a two-year Master of Public Policy (MPP) degree, the first MPP program in Florida. The institute has established the state's first dual-degree programs:
- MPP-Juris Doctor (JD)
- MPP-Master of Business Administration (MBA)
- MPP-Master of Science in Marine Science (MS).
- Marine Science Research Institute (MSRI): Specializing in the mouth of the St. Johns River and coastal marine ecosystems, MSRI holds a LEED Gold certification. JU aims to create a leading educational center for research in biology and the marine environment in northeast Florida. JU has offered a Bachelor's degree in Marine Science since 1978 and provides Master of Arts and Master of Science degrees in Marine Science.
- STEAM Institute: It is a human-centered, project-based learning environment where students from various disciplines engage in design thinking and practical problem-solving.
- UpSkill Institute: Expanding opportunities for continuous education in the most in-demand skills, knowledge, and technical skills. There are hundreds of courses to help students gain an edge in the competitive economy.