Abstract: We propose a new way of analyzing pupil measurements made in conjunction with eye tracking: fixation-aligned pupillary response averaging, in which short windows of continuous pupil measurements are selected based on patterns in eye tracking data, temporally aligned, and averaged together. Such short pupil data epochs can be selected based on fixations on a particular spot or a scan path. The windows of pupil data thus selected are aligned by temporal translation and linear warping to place corresponding parts of the gaze patterns at corresponding times and then averaged together. This approach enables the measurement of quick changes in cognitive load during visual tasks, in which task components occur at unpredictable times but are identifiable via gaze data. We illustrate the method through example analyses of visual search and map reading. We conclude with a discussion of the scope and limitations of this new method.