3D representations in applications that provide self-localization and orientation in wayfinding have become increasingly popular in recent years because of technical advances in the field. However, human factors have been largely ignored while designing 3D representations in support of pedestrian navigation. This exploratory study aims to explore gender effects on using 3D maps for spatial orientation. We designed a 3D map that combines salient 3D landmarks and 2D layouts, and evaluated gender differences in their performance during direction-pointing tasks by administrating an eye tracking experiment. The results indicate there was no significant overall gender difference on performance and visual attention. However, we observed that males using the 3D map paid more attention to landmarks in the environment and performed better than when using the conventional 2D map, whereas female performance did not show any significant difference between the two types of map usage. We also observed contrary gender differences in visual attention on landmarks between the 3D and 2D maps. While males fixated longer on landmarks than females when using the 3D map, females paid more visual attention to landmarks than males when using the 2D map. In addition, verbal protocols showed that males had more confidence while make decisions. These empirical results can be helpful in the design of map-based wayfinding enhancement tools.