Intraductal papillary mucinous neoplasms (IPMN) are cystic neoplasms of the pancreatic ductal system. These incidental cystic lesions are increasingly found on radiological imaging and screened for malignant transformation. The Fukuoka consensus guidelines recommend screening with computed tomography, magnetic resonance imaging or endoscopic ultrasound. Branch duct IPMN (BD-IPMN) have significantly lower malignancy and mortality rates compared to main duct IPMN. Our aim was to assess the cost-effectiveness of guideline's recommendations for BD-IPMN screening of cysts between 2 and 3 cm in an Australian context. Markov model decision analysis was used to calculate the incremental cost-effectiveness ratio (ICER) of screening. The ICER was compared to a willingness to pay (WTP) threshold of $50 000. We performed scenario analysis to examine the effect of cyst size and non-linearity of malignancy rate on ICER. Probabilistic sensitivity analyses (PSA) were performed on our input parameters. Screening resulted in 586 quality adjusted life years gained and a net present value of $20 379 939, resulting in a base-case ICER of $34 758. After scenario analysis for non-linearity of malignancy rate the ICER increases to $64 555, which is above the WTP threshold. PSA indicates that ICER is most susceptible to the pre-test malignancy rate. This cost analysis demonstrates that screening of 2-3 cm BD-IPMN according to current guidelines is unlikely to be cost-effective in an Australian context. To determine the true ICER, a cost analysis on real-world data is required.