Studies of gender-related differences in the perception of ecommerce websites dependent on the websites' aesthetics, usefulness, ease of use, and purchase intentions, give contradictory results. To shed light on these conflicting findings, in addition to self-reported data from two online questionnaires (Study 1 & Study 2), our research uses the neuroimaging method of functional near-infrared spectroscopy to explore possible gender-related differences (Study 3). By conducting three studies, users’ conscious and unconscious (neural) evaluations of ecommerce websites are explored. The self-reported results reveal that men and women do not significantly differ in their expressed evaluations of ecommerce websites. However, the neural results indicate that gender-related differences in the perception of ecommerce websites are influenced by unconscious effects, which might explain the inconsistent gender-specific research findings. Men tend to require greater neural activity when using ecommerce websites. Websites evaluated as useful and visually aesthetic lead to significant neural activation in brain regions of the left hemisphere for men in comparison to women, whereas websites evaluated as less useful and appealing reveal neural activation in brain regions of the right hemisphere in male participants. The results provide several theoretical and practical implications for the evaluation of gender-specific decision making on ecommerce websites.