Dysregulation of the autonomic nervous system (ANS) is commonly observed in various mental disorders, particularly when individuals engage in prolonged cognitive‐emotional tasks that require ANS adjustment to workload. Although the understanding of the temporal dynamics of sympathetic and parasympathetic tones in obsessive‐compulsive disorder (OCD) is limited, analyzing ANS reactions to cognitive‐emotional workload could provide valuable insights into one of the underlying causes of OCD. This study investigated the temporal dynamics of heart rate (HR) and pupil area (PA) while participants with OCD and healthy volunteers solved antisaccade tasks, with affective pictures serving as central fixation stimuli. The data of 31 individuals with OCD and 30 healthy volunteers were included in the study, comprising three separate blocks, each lasting approximately 8 min. The results revealed an increase in sympathetic tone in the OCD group, with the most noticeable rise occurring during the middle part of each block, particularly during the presentation of negative stimuli. Healthy volunteers demonstrated adaptive temporal dynamics of HR and PA from the first block to the last block of tasks, whereas individuals with OCD exhibited fewer changes over time, suggesting a reduced adaptation of the ANS sympathetic tone to cognitive‐emotional workload in OCD.