Previous studies have witnessed that complex brain networks have the properties of high global and local efficiency. In this study, we investigated the gender effect on brain functional networks measured using functional magnetic resonance imaging (fMRI). Our experimental results showed that there were no significant difference in global and local efficiency between male and female. However, the gender-related effects on nodal efficiency were found at several brain regions, including the left middle frontal gyrus, right superior temporal gyrus, left middle cingulum gyrus, left hippocampus, right hippocampus, right parahippocampal and left amygdala. These results were compatible with previous findings. To our knowledge, this study provided the first evidence of gender effect on the efficiency of brain functional networks using resting-state fMRI.