Psychophysiological responses have been studied as objective indicators for measuring a learner's cognitive load. Previous studies have correlated pupil dilation or fixation length with increased cognitive load. Our aims were to confirm whether these findings could be applied in a general learning context and to verify the additivity hypothesis of cognitive load theory based on psychophysiological responses. Three responses (i.e., mean pupil diameter, area under the pupil response curve, and sum of fixation duration) were recorded while 94 participants completed a computer-based test. Participants were randomly assigned to low (n = 46) or high (n = 48) extraneous cognitive load conditions. Because the given test, which consisted of a low and a high task complexity problem, was the same for all participants, the difference in intrinsic cognitive load was compared as a within-subjects factor. Each psychophysiological indicator was calculated and compared under different intrinsic and extraneous cognitive load conditions. The results showed that psychophysiological responses significantly distinguished the differences in intrinsic and extraneous cognitive loads. In addition, the sum of the different types of cognitive loads corresponded to the total cognitive load. Based on the results, further studies are suggested to apply psychophysiological responses as the standard of judgment for different levels of cognitive load.