In chronometric mental rotation tasks, sex differences are widely discussed. Most studies find men to be more skilled in mental rotation than women, which can be explained by the holistic strategy that they use to rotate stimuli. Women are believed to apply a piecemeal strategy. So far, there have been no studies investigating this phenomenon using eye-tacking methods in combination with electroencephalography (EEG) analysis: the present study compared behavioral responses, EEG activity, and eye movements of 15 men and 15 women while solving a three-dimensional chronometric mental rotation test. The behavioral analysis showed neither differences in reaction time nor in the accuracy rate between men and women. The EEG data showed a higher right activation on parietal electrodes for women and the eye-tracking results indicated a longer fixation in a higher number of areas of interest at 0° for women. Men and women are likely to possess different perceptual (visual search) and decision-making mechanisms, but similar mental rotation processes. Furthermore, men presented a longer visual search processing, characterized by the greater saccade latency of 0°–135°. Generally, this study could be considered a pilot study to investigate sex differences in mental rotation tasks while combining eye-tracking and EEG methods.