AbstractHow the brain represents gender identity is largely unknown, but some neural differences have recently been discovered. We used an intrinsic ignition framework to investigate whether there are gender differences in the propagation of neural activity across the whole‐brain and within resting‐state networks. Studying 29 trans men and 17 trans women with gender incongruence, 22 cis women, and 19 cis men, we computed the capability of a given brain area in space to propagate activity to other areas (mean‐ignition), and the variability across time for each brain area (node‐metastability). We found that both measurements differentiated all groups across the whole brain. At the network level, we found that compared to the other groups, cis men showed higher mean‐ignition of the dorsal attention network and node‐metastability of the dorsal and ventral attention, executive control, and temporal parietal networks. We also found higher mean‐ignition values in cis men than in cis women within the executive control network, but higher mean‐ignition in cis women than cis men and trans men for the default mode. Node‐metastability was higher in cis men than cis women in the somatomotor network, while both mean‐ignition and node‐metastability were higher for cis men than trans men in the limbic network. Finally, we computed correlations between these measurements and a body image satisfaction score. Trans men's dissatisfaction as well as cis men's and cis women's satisfaction toward their own body image were distinctively associated with specific networks in each group. Overall, the study of the whole‐brain network dynamical complexity discriminates gender identity groups, functional dynamic approaches could help disentangle the complex nature of the gender dimension in the brain.