Gastrointestinal (GI) symptoms such as bloating, constipation, and nausea are common in the days before menstruation, experienced by as many as 73 % of menstruating individuals. Mood may influence the link between menstrual cycle and GI symptoms, with prior studies indicating that even among healthy controls, GI symptoms worsen premenstrually and are associated with worsening mood. Associations between GI symptoms and mood are poorly understood among those with premenstrual syndrome (PMS), a cluster of mood and/or physical symptoms that occur in the week before menses affecting roughly 20 % of menstruators. Our primary aim was to examine associations between GI symptoms and mood symptoms across the menstrual cycle, in those who do and do not report PMS using a menstrual tracking app. We hypothesized that GI symptoms would be reported more frequently in the luteal phase than follicular phase, and that frequency of GI symptoms would be positively associated with mood symptoms in those with PMS. We analyzed data from 33,628 menstrual cycles across 32,241 participants, including n = 27,897 controls (29,137 menstrual cycles) and n = 4344 PMS participants (4491 menstrual cycles). GI symptoms were reported significantly more frequently in the luteal phase than the follicular phase in both control and PMS groups (p < 0.001). Mood symptoms were significantly positively associated with GI symptoms in both groups, in both follicular and luteal phases (p < 0.001). Results suggest that premenstrual GI symptoms are a common issue, and additional work is needed to explore associations between mood and GI symptoms in the context of the menstrual cycle.