The College of Arts & Sciences encompasses the divisions of Humanities, Science and Mathematics, Social Sciences, pre-professional and Navy ROTC programs.
 
The Davis College of Business contains the Division of Accounting, Economics, and Finance; the Division of Management, Marketing, and International Business; and the Division of Aeronautics.
The Davis College of Business prepares students to enter the dynamic and complex world of business. The philosophy that guides the educational process is to provide the working knowledge necessary for success in an organization, and to integrate this knowledge from the various disciplines of accounting, finance, economics, marketing, and management into a meaningful whole. Theory is combined with a practical and pragmatic approach to the effective and efficient utilization of resources. Careful attention is given to the increasing importance of resource scarcity and an understanding of the global environment in which the business community operates.
The mission of the Davis College of Business is to deliver high quality business programs that emphasize leadership development, foster global and multicultural awareness, and build upon a foundation in the liberal arts and humanities. The College will create and disseminate applied business knowledge that contributes to the advancement of business education and practice.
 
College of Fine Arts
The College of Fine Arts is dedicated to giving to each individual student the instruction and guidance needed to realize his or her full artistic and intellectual potential, and provide each student with ongoing opportunities for performance and exhibition, as well as personal attention. The College has three divisions: the Division of Visual Arts; the Division of Music; and the Division of Theatre and Dance.
 
College of Health Sciences
The College of Health Sciences is home to the School of Nursing, Sport and Exercise Science and Communication Sciences and Disorders.​
 
School of Nursing​
The School of Nursing offers two (2) Commission on Collegiate Nursing Education (CCNE) accredited programs that lead to a Bachelor of Science in Nursing (BSN) degree or a Masters of Science in Nursing (MSN) degree.
Consistent with the mission of Jacksonville University, the School of Nursing is dedicated to the success of each student as a self-assured, competent professional nurse who can practice in the global community. The Bachelor of Science in Nursing (BSN) degree is based on a strong liberal arts and science foundation and is offered to traditional and nontraditional students. The School of Nursing prepares professional nurses who make compassionate, sound decisions regarding care to individuals, families, and communities in a culturally diverse society. Graduates provide quality care through effective communication, critical thinking, and collaboration with other professionals. Graduates are prepared to become responsible citizens and leaders in their communities and profession through active involvement in and appreciation for lifelong learning.
 
School of Education
The School of Education (SOE) undergraduate programs are comprised of two departments: Education and Physical Education. Students may major in Elementary and Physical Education Teaching Preparation (M.Ed./B.S. degree).
The SOE offers three (3) Minors: Education, Coaching, or Exercise Science. Students must be enrolled in an appropriate major at JU and work with the SOE to create a program of study. The Education Minor leads to fulfillment of Florida Department of Education’s (FLDOE) certification requirements.
Each academic program incorporates the SOE’s connected-learning approach to education through supportive faculty-teacher relationships, curriculum based on current practice and research, and varied field-based experiences. These programs are geared towards traditional age or transfer students.
The SOE also offers a Masters of Education in Leadership and Learning with three concentrations: Instructional Leadership and Organizational Design, Sport Management and Leadership, and Educational Leadership (Aspiring Principals). The Educational Leadership concentration is a FLDOE State Approved program. All three concentrations are completed within 18 months.
 
School of Orthodontics
The Advanced Specialty Education Program in Orthodontics and Dentofacial Orthodontics offers a 24-month certificate program through the School of Orthodontics. The program combines didactic, clinical, and research components, leading to a Certificate of Advanced Graduate Study (C.A.G.S.) in Orthodontics. Students must be prepared to undertake an intensive, continuous, full-time course of study in addition to heavy supervised clinical training in various contemporary orthodontic techniques.
Classes begin in mid-August of each year. By the end of the first year it is expected that each student will have initiated comprehensive orthodontic treatment for at least fifty patients after completion of a pre-clinical training course. Students are introduced to a variety of treatment philosophies, with an emphasis on pre-adjusted appliances and related techniques. Supervising clinical faculty present their philosophies in daily diagnosis and treatment planning seminars. A variety of clinical techniques are demonstrated and utilized in the school’s state-of-the-art orthodontic clinical facility.
 
The mission of the College of Interdisciplinary and Professional Studies (CIPS) is to provide high-quality educational programs to equip students with the knowledge and skills to become productive, responsible citizens and ethical leaders in their local, national and global communities.
 
CIPS offers interdisciplinary degrees in Sustainability and Public Policy. The college offers a Bachelor of Science, Bachelor of Arts and Bachelor of Business Administration in Sustainability. In addition, its JU Public Policy Institute offers a two-year Masters in Public Policy (MPP) degree, which is the first MPP Program in Florida. In addition, the Institute has established the first Master in Public Policy dual degree programs in the state. This includes the Master in Public Policy-Juris Doctor in conjunction with Florida Coastal School of Law (MPP-JD), Master in Public Policy-Master of Business Administration (MPP-MBA) and Master of Public Policy-Marine Science (MPP-MS) joint degree programs. 
The college also houses the Accelerated Degree Program (ADP), as well as stand-alone M.Ed. degrees in Curriculum and Instruction and Instructional Leadership and Organizational Development.