Gender differences were identified in the frequency and clinical presentations of inflammatory bowel disease (IBD) and depressive and anxiety disorders, which are more common in IBD patients than in the general population. The present manuscript provides a critical overview of gender differences in the frequency and clinical course of mood and anxiety disorders in IBD patients, with the aim of helping clinicians provide individualized management for patients. All of the included studies found that IBD patients reported a higher frequency of depressive and anxiety disorders than the general population. These findings should encourage healthcare providers to employ validated tools to monitor the mental health of their IBD patients, such as the Patient Health Questionnaire (PHQ-9). In addition, most studies confirm that women with IBD are more likely than men to develop affective disorders and show that up to 65% of women with IBD have depressive and anxiety disorders. Women with IBD require close mental health monitoring and ultimately a multidisciplinary approach involving mental health professionals. Drug treatment in women should be individualized and medications that may affect mental health (e.g., corticosteroids) should be thoroughly reconsidered. Further data are needed to ensure individualized treatment for IBD patients in a framework of precision medicine.