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Functional magnetic resonance imaging (fMRI) has been used to investigate sex‐related differences in brain abnormalities in patients with irritable bowel syndrome (IBS). Like IBS, women with functional constipation (FC) are 2.1 times as many as men. No study has been performed yet to examine sex‐related differences in brain activity and connectivity in patients with FC. Here, we employed resting‐state fMRI with amplitude of low‐frequency fluctuation (ALFF) to investigate brain functional differences in 51 patients with FC (34 females) and 52 healthy controls (34 females). Results showed abdominal pain and abdominal distension correlated with trait (TAI) and state (SAI) anxiety ratings in the female FC group, and abdominal distension correlated with sensation of incomplete evacuation in the male FC group. Two‐way ANOVA revealed sex effects on ALFF in precentral gyrus, thalamus, insula (INS), and orbital …