Despite the presence of various guidelines, diagnosing malignant intraductal papillary mucinous neoplasm (IPMN) continues to pose challenges. Furthermore, although endoscopic ultrasonography (EUS) offers high-resolution images, it has not yet recognized as the primary tool for malignancy diagnosis. The study objective was to develop a simplified and user-friendly scoring system to improve the diagnostic accuracy of malignant IPMNs. Additionally, the utility of EUS and its effect on diagnostic accuracy were assessed. We retrospectively collected the clinical data on 160 cases of resected IPMN at Tokyo Medical and Dental University Hospital from January 2008 to December 2022. We examined clinical features, computed tomography (CT) and magnetic resonance imaging (MRI) findings, and EUS results if available. We then calculated the odds ratio of malignancy for these factors and developed an IPMN malignancy prediction (IMAP) scoring system. There were 89 (55.6%) cases of benign IPMNs and 71 (44.4%) of malignant IPMNs. Eight clinical and imaging findings, including age, diabetes mellitus status, jaundice, CA19-9 level, enhancing mural nodules ≥5mm, thickened wall, and main duct dilatation, were significantly associated with malignancy. The IMAP score was calculated by assigning 0 to 2 points to these factors based on the odds ratio. The area under the receiver operating characteristic curve for the IMAP score was 0.78 [95% confidence interval (CI): 0.71-0.85] based on CT/MRI alone and improved to 0.81 (95% CI: 0.74-0.87) when EUS was added. When the total exceeds 5 points, the positive predictive value becomes 100% (95% CI: 95.9-100). In conclusion, the IMAP scoring system has demonstrated promise as a clinically useful tool, offering both simplicity and sufficient accuracy. It holds potential as an important decision criterion for determining the treatment approach for IPMN. Additionally, EUS contributes to enhancing the diagnostic accuracy of the IMAP scoring system, thereby enabling more precise decision-making.