Distinguishing colorectal from gastroduodenal perforations is clinically important and challenging. We aimed to establish a scoring model based on objective findings (excluding computed tomography findings) for the diagnosis of colorectal perforation and its differentiation from gastroduodenal perforation. Patients diagnosed with colorectal or gastroduodenal perforations between January 2014 and December 2021 were retrospectively studied. Univariate and multivariate analyses were performed to identify independent variables, and a scoring model was developed based on these variables. Among 131 eligible patients, 64 (48.9%) were in the colorectal group and 67 (51.1%) were in the gastroduodenal group. White blood cell count, C-reactive protein, and quick Sequential Organ Failure Assessment score were identified as independent clinical variables associated with the diagnosis of colorectal perforation, which differentiated colorectal perforation from gastroduodenal perforation, and were used to develop a new scoring model. The scores ranged from 0 to 5, with an area under the receiver operating characteristic curve of 0.846. The probabilities of colorectal perforation with scores of 0, 1.5, 2, 3, 3.5, and 5 were 3.2, 20, 55.6, 81.8, 73.9, and 82.4%, respectively. The new scoring model may help in treatment selection and perioperative management of patients with gastrointestinal perforation.