Insular cortex (INS) plays a critical role in pain processing and shows sex differences in functional activation during noxious visceral stimulation. Less is known regarding functional interactions within the INS and between this structure and other parts of the brain. Cerebral blood flow mapping was performed using [14C]-iodoantipyrine perfusion autoradiography in male and female rats during colorectal distension (CRD) or no distension (controls). Forty regions of interest (ROIs) were defined anatomically to represent the granular, dysgranular, and agranular INS along the anterior-posterior (A-P) axis. Inter-ROI correlation matrices were calculated for each group to characterize intra-insular functional connectivity (FC). Results showed a clear FC segregation within the INS into an anterior (rostral to bregma +2.4 mm), a posterior (caudal to bregma −1.2 mm), and a mid INS subregion in between. Female controls showed higher FC density compared to males. During CRD, intra-insular FC density decreased greatly in females, but only modestly in males, with a loss of long-range connections between the anterior and mid INS noted in both sexes. New functional organization was characterized in both sexes by a cluster in the mid INS and primarily short-range FC along the A-P axis. Seed correlation analysis during CRD showed sex differences in FC of the anterior and mid agranular INS with the medial prefrontal cortex, thalamus, and brainstem areas (periaqueductal gray, parabrachial nucleus), suggesting sex differences in the modulatory aspect of visceral pain processing. Our findings suggest presence of substantial sex differences in visceral pain processing at the level of the insula.