The purpose of this exploratory study was to determine whether learning preferences of secondary students identified with concomitant learning disabilities (LD) and emotional disturbance (ED) align with the instructional method with which they best learned mathematics. Responses to a preference survey given before and after instruction were compared with learning outcomes in a single-subject, alternating treatments research design investigating the effects of direct teach, computer-assisted instruction (CAI), and a combination of both methods. Results showed that most students were able to predict, by choice or stated preference, conditions under which they will learn best and, in hindsight, indicate the condition that provided the best learning outcome. This small study contributes to the literature on secondary mathematics learning for students with LD, and makes unique contributions regarding (a) the learning of students with comorbid LD and ED and (b) implementation of instruction that combines direct teach with CAI.