Background: The clinical and epidemiological features of bipolar disorder (BD) between females and males have many differences. The association between brain function and gender in BD is unknown. This research aimed to investigate the association between brain function and gender in BD by using amplitude of low-frequency fluctuations (ALFFs). Methods: Ninety-eight patients (49 females and 49 males) with BD and 171 matched healthy controls (HCs, 89 females and 82 males) were recruited for resting-state functional magnetic resonance imaging. ALFF was used to estimate brain function. Results: A main effect of diagnosis in ALFF was observed in the dorsal lateral prefrontal cortex (DLPFC), ventral prefrontal cortex (VPFC), caudate and occipital lobe. A main effect of gender in ALFF was found in the right VPFC, DLPFC, thalamus, and occipital lobe. A main effect of diagnosis gender interaction in ALFF was observed in the left DLPFC. Analyses of two-sample t-test indicated that male patients with BD had increased ALFF in the right hippocampus, right amygdala, left caudate, and left DLPFC, and decreased ALFF in the occipital lobe compared with male HC. Female patients with BD demonstrated increased ALFF in the right VPFC and right DLPFC compared with female HC. Male patients with BD exhibited increased ALFF in the right VPFC and left DLPFC and decreased ALFF in the occipital lobe compared with female patients with BD. Limitations: This study did not consider the effect of medications and emotional states on brain activity. Conclusions: Results suggested gender differences in the dysfunctions of the cortico-limbic neural system in BD.