As students matriculate into the upper grades, they will begin to access the Honors and AP ("Advanced Placement") courses offered in each department. At any one time, over 85% of the 10th through 12th grade students take at least one Honors or AP level class. All Honors classes are U.C. accredited as AP level courses. The synthesis of Honors and AP course designations reflects Flintridge Prep's efforts to maintain a balance between the ideals of the classroom experience and the requirements and expectations of a rigorous college preparatory environment.

Flintridge students excel in the A.P. testing system. In 2007, approximately 74% of the students in the 10th through 12th grades took, on average, two AP exams from among 16 subject areas. Ninety-five percent (95%) of the tests resulted in a passing grade of 3 or above. Among the 214 students who took an A.P. exam, 35 were designated A.P. Scholars, 22 were designated A.P. Scholars with Honor, 54 were designated A.P. Scholars with Distinction, and 6 were designated National Scholars. The school average A.P. grade was 4.29.