Recent evidence challenges the typical notion that men outperform women in mental rotation (MR) tasks, possibly due to the use of experimental protocols that either used only two types of MR images or where gender was added post hoc as a factor. The present study investigated how the interaction between gender and stimulus type affects the brain activity related to MR tasks. fMRI data were recorded while participants performed MR of abstract objects, real objects, and bodily figures. With respect to women, men had stronger inferior frontal activations during MR of abstract objects, and in superior and medial frontal areas during MR of bodily figures. Compared to men, women showed stronger activation in the superior parietal lobe during MR of bodily figures with respect to abstract objects, and in the right inferior occipital cortex in the MR of real objects versus bodily figures. Finally, men showed a positive relationship between accuracy and brain activity in the right precuneus, while women showed a negative relationship between accuracy and brain activity in right motor and premotor areas. These results show that brain activity during MR is modulated by the type of images, differently for women and men.