At the end of each semester, each dean receives the names of full-time (12 units or more) honor students. Those with a GPA of 3.65 or higher receive First Honors; those with 3.40 to 3.64 receive Second Honors. All honor students receive a personal commendation letter from the appropriate dean.

Students of outstanding academic merit receive special honors at graduation. Eligibility for these special honors is based upon USD GPA: a) for summa cum laude, 3.90 or higher; b) for magna cum laude, 3.70 to 3.89; and c) for cum laude 3.50 to 3.69. The senior with the highest USD GPA within each commencement group will give the valedictory address at his/her respective ceremony. At least half of the degree work must be completed at USD. In the event of ties, the student with the most coursework completed at USD will give the valedictory address at his/her respective ceremony. Also presented at graduation are the Alcalá Leadership Awards to two outstanding seniors.

At the annual University of San Diego Honors Convocation, a formal year-end assembly, awards are presented to a number of students who have shown exceptional attainment in academic and other areas of university life. Departmental honors are awarded to seniors who have petitioned to graduate and have maintained a USD grade point average of 3.5 in upper division courses in their major, provided that a minimum of 12 such units have been completed at USD prior to February 1 of the year of graduation. However, a student may lose eligibility for special honors and departmental honors if the student has been found to have committed a serious violation of the academic integrity policy.