Intraductal papillary mucinous neoplasms (IPMNs) are a heterogeneous group of neoplasms and represent the most common identifiable precursor lesions of pancreatic cancer. Clinical decision-making of the risk for malignant disease, including high-grade dysplasia and invasive carcinoma, is challenging. Moreover, discordance on the indication for resection exists between the contemporary guidelines. Furthermore, most of the current nomogram models for predicting malignant disease depend on endoscopic ultrasonography to evaluate the precise size of mural nodules. Thus, this study aimed to propose a model to predict malignant disease using variables from a noninvasive examination. We evaluated patients who underwent resection of pathologically confirmed IPMNs between November 2010 and December 2018 and had preoperative clinical data available for review. Based on binary multivariable logistic regression analysis, we devised a nomogram model to predict malignant IPMNs. The area under the receiver operating characteristics curve (AUC) was used to evaluate the discrimination power of the model. Of the 333 patients who underwent resection of IPMNs, 198 (59.5%) had benign and 135 (40.5%) had malignant IPMNs. Multivariable logistic regression analysis showed that cyst size, cyst location, cyst wall enhancement, multicystic lesion, diameter of main pancreatic duct, neutrophil-to-lymphocyte ratio, serum carbohydrate antigen 19-9, and carcinoembryonic antigen were significantly associated with malignancy. The nomogram, constructed based on these variables, showed excellent discrimination power with an AUC of 0.859 (95% CI: 0.818–0.900, P < 0.001). In conclusion, we have developed a nomogram consisting of a combination of cross-sectional imaging features and blood markers, variables that can readily be obtained by noninvasive examinations during the surveillance period, which can distinguish benign from malignant IPMNs. Nevertheless, external validation is warranted.