Pancreatic radiation effect (PRE) can be a component of gastrointestinal tract (GIT) radiotoxicity. This inter-organ correlation between the GIT and the pancreas was assessed through a rat model. Separate local irradiation to the abdomen and the pelvis was applied concurrently for 8-week-old male Sprague Dawley rats. Abdominal irradiation was categorized into pancreatic shield (PS) and non-pancreatic shield (NPS) irradiation. After 5 Gy and 15 Gy irradiation, the rectal mucosa was analyzed at the first week (early phase, Ep) and the 14th week (late phase, Lp). A slow gain in body weight was observed initially, particularly in the NPS group receiving a 15 Gy dose (P < 0.001). The large number of apoptotic bodies after 15 Gy at Ep decreased at Lp. At Ep for the 5-Gy group, the NPS group revealed more fibrotic change than the PS group (P = 0.002). Cleaved caspase-3 (CCP3) expression was greater at Lp, and the Ep–Lp increase was prominent in the NPS-15-Gy group (P = 0.010). At Lp, for 15 Gy irradiation, CCP3 was expressed more in the NPS group than in the PS group (P = 0.032). Despite no direct toxicity difference between the PS and NPS groups, small changes in parameters such as fibrosis or CCP3 expression suggest that pancreatic shielding does have an effect on the radiation response in the rectal mucosa, which suggests a need for a multi-organ effect-based approach in GIT radiotoxicity assessment.