The purpose of the study was to examine the effects of instruction given with different multimedia modalities (written text + animation or narration + animation) on the academic achievement, cognitive load, and positive affect in different paces (learner-paced or system-paced); 97 freshmen university students divided into four groups taught in different modalities and paces. These groups are written text + animation and learner-paced (WA + L), written text + animation and system-paced (WA + S), narration + animation and learner-paced (NA + L), and narration + animation and system-paced (NA + S). The findings did not reveal any significant difference between the achievements of the groups. Within the context of cognitive load, modality principle in learner-paced groups was confirmed. Instruction conducted with different multimedia modalities in different paces did not cause any difference between the positive affects of the groups. However, in contrast with the other three groups, the positive affects of the students studying with the NA+ L software increased in the posttest when compared with those in the pretest.