Freshman Academy is a required program for first-year students who are accepted to William Jessup University on academic support. The program is two semesters, where students are registered as a cohort. Academy students receive early registration for fall and spring and a variety of academic support services to enable them to graduate in four years.

The Transfer Academy is a one-semester program required for incoming transfer students who are accepted to William Jessup University on academic support. Students are registered in a one-unit support course in addition to their first semester classes and are able to remain on track toward graduation.